|
| 10320. Myr-Arf1 conformational flexibility at the membrane surface:
insights for ArfGAP ASAP1 interactions.
Y. Zhang, O. Soubias, Shashank Pant, F. Heinrich, A. Vogel, J. Li, Y. Li, L. A.
Clifton, S. Daum, K. Bacia, D. Huster, P. A. Randazzo, M. Lösche, Emad
Tajkhorshid, and R. A. Byrd.
Nature Communications, 2023.
In Press.
|
| 10319. VMD as a platform for interactive small molecule preparation and
visualization in quantum and classical simulations.
Mariano Spivak, John E. Stone, Jo ao Ribeiro, Jan Saam, Peter L. Freddolino,
Rafael C. Bernardi, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 63:4664-4678,
2023.
Published.
|
| 10318. Quinoline thiourea-based zinc ionophores with antibacterial activity.
Subhasis Dey, Anjali Patel, Nandan Haloi, Soumya Srimayee, Suman Paul,
Ganesh Kumar Barik, Nasim Akhtar, Dipanjan Shaw, Gunanka Hazarika,
Biswa Mohan Prusty, Mohit Kumar, Manas Kumar Santra, Emad Tajkhorshid,
Surajit Bhattacharjee, and Debasis Manna.
Journal of Medicinal Chemistry, 66:11078-11093, 2023.
Published.
|
| 10316. Structures and membrane interactions of native serotonin transporter
in complexes with psychostimulants.
Dongxue Yang, Zhiyu Zhao, Emad Tajkhorshid, and Eric Gouaux.
Proceedings of the National Academy of Sciences, USA,
120:e2304602120, 2023.
Published.
|
| 10315. End-to-end AI framework for interpretable prediction of molecular
and crystal properties.
Hyun Park, Ruijie Zhu, E. A. Huerta, Santanu Chaudhuri, Emad Tajkhorshid, and
Donny Cooper.
Machine Learning: Science and Technology, 4:025036, 2023.
Published.
|
| 10314. Insights into substrate transport and water permeation in the
mycobacterial transporter MmpL3.
Yupeng Li, Atanu Acharya, Lixinhao Yang, Jinchan Liu, Emad Tajkhorshid,
Helen I. Zgurskaya, Mary Jackson, and James C. Gumbart.
Biophysical Journal, 122:2342-2352, 2023.
Published.
(PMC: PMC10257117) |
| 10317. Application experiences on a gpu-accelerated arm-based hpc testbed.
Wael Elwasif, William Godoy, Nick Hagerty, J. Austin Harris, Oscar Hernandez,
Balint Joo, Paul Kent, Damien Lebrun-Grandie, Elijah Maccarthy,
Veronica Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei
Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan,
Rene Widera, Spencer Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey
Young, Sunita Chandrasekaran, Florina Ciorba, Osman Simsek, Kate Clark,
Filippo Spiga, Jeff Hammond, John Stone, David Hardy, Sebastian Keller,
Jean-Guillaume Piccinali, and Christian Trott.
In Proceedings of the HPC Asia 2023 Workshops, HPC Asia '23
Workshops, pp. 35-49, New York, NY, USA, 2023. Association for Computing
Machinery.
|
| 10309. Cryo-EM structures of human ABCA7 provide insights into its
phospholipid translocation mechanisms.
Le Thi My Le, James R. Thompson, Sepehr Dehghani-Ghahnaviyeh, Shashank Pant,
Phuoc X. Dang, Takahisa Kanikeyo, Emad Tajkhorshid, and Amer Alam.
EMBO Journal, 42:e111065, 2023.
(PMC: PMC9890230) |
| 10313. Tuning phenylalanine fluorination to assess aromatic contributions to
protein function and stability in cells.
Grace D. Galles, Daniel T. Infield, Colin J. Clark, Marcus L. Hemshorn, Shivani
Manikandan, Frederico Fazan, Ali Rasouli, Emad Tajkhorshid, Jason D. Galpin,
Richard B. Cooley, Ryan A. Mehl, and Christopher A. Ahern.
Nature Communications, 14, 2023.
Published.
(PMC: PMC9813137) |
| 10310. Backbone amides are key determinants of Cl− selectivity in
CLC ion channels.
Lilia Leisle, Kin Lam, Sepehr Dehghani-Ghahnaviyeh, Eva Fortea, Jason Galpin,
Christopher A. Ahern, Emad Tajkhorshid, and Alessio Accardi.
Nature Communications, 13, 2022.
Published.
(PMC: PMC9726985) |
| 10307. Lipid-mediated prestin organization in outer hair cell membranes and
its implications in sound amplification.
Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, and Emad Tajkhorshid.
Nature Communications, 13, 2022.
(PMC: PMC9653410) |
| 10308. Differential dynamics and direct interaction of bound ligands with
lipids in multidrug transporter ABCG2.
Ali Rasouli, Qin Yu, Sepehr Dehghani-Ghahnaviyeh, Po-Chao Wen, Julia Kowal,
Kaspar Lochar, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
120:e2213437120, 2022.
Published.
|
| 10312. #COVIDisAirborne: AI-enabled multiscale computational microscopy
of delta SARS-CoV-2 in a respiratory aerosol.
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer,
Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda
Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra
Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa
Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith,
Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick Manby, Anima
Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David
Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher
Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard
Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas
Miller, Shantenu Jha, Arvind Ramanathan, Lillian Chong, and Rommie Amaro.
The International Journal of High Performance Computing
Applications, 37:10943420221128233, 2022.
(PMC: PMC8609898) |
| 10305. Structures of the TMC-1 complex illuminate mechanosensory
transduction.
H. Jeong, S. Clark, A. Goehring, Sepehr Dehghani-Ghahnaviyeh, Ali Rasouli, Emad
Tajkhorshid, and Eric Gouaux.
Nature, 610:796-803, 2022.
(PMC: PMC9605866) |
| 10304. Proton-driven alternating access in a spinster lipid transporter.
Reza Dastvan, Ali Rasouli, Sepehr Dehghani-Ghahnaviyeh, Samantha Gies, and Emad
Tajkhorshid.
Nature Communications, 13, 2022.
|
| 10291. Intelligent resolution: Integrating cryo-EM with AI-driven
multi-resolution simulations to observe the SARS-CoV-2
replication-transcription machinery in action.
Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim
Zvyagin, Heng Ma, Austin Clyde, David Clark, David J. Hardy, Tom Burnley, Lei
Huang, John McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis
Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey
Wells, Venkatesh Mysore, Thomas Gibbs, James Phillips, S. Chakra
Chennubhotla, Ian Foster, Rick Stevens, Anima Anandkumar, Venkatram
Vishwanath, John E. Stone, Emad Tajkhorshid, Sarah A. Harris, and Arvind
Ramanathan.
The International Journal of High Performance Computing
Applications, 36:603-623, 2022.
|
| 10306. Molecular view into preferential binding of the factor VII gla
domain to phosphatidic acid.
Melanie P. Muller, James H. Morrissey, and Emad Tajkhorshid.
Biochemistry, 61:1694-1703, 2022.
|
| 10301. Phthalate monoesters act through peroxisome proliferator-activated
receptors in the mouse ovary.
Daryl D. Meling, Kathy M. De La Torre, Andres S. Arango, Andressa Gonsioroski,
Ashley R. K. Deviney, Alison M. Neff, Mary J. Laws, Genoa R. Warner, Emad
Tajkhorshid, and Jodi A. Flaws.
Reproductive Toxicology, 110:113-123, 2022.
|
| 10303. Targeting lipid-protein interaction to treat Syk-mediated acute
myeloid leukemia.
I. Singaram, A. Sharma, S. Pant, M. Lihan, M.-J. Park, P. Buwaneka, Y. Hu,
N. Mahmud, Y.-M. Kim, V. Gevorgyan, I. Khan, Emad Tajkhorshid, and W. Cho.
Nature Chemical Biology, 19:239-250, 2023.
Published.
(PMC: PMC9898191) |
| 10302. py-MCMD: Python software for performing hybrid monte
carlo/molecular dynamics simulations with GOMC and NAMD.
Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy,
John E. Stone, Loren Schwiebert, Jeffrey Potoff, and Emad Tajkhorshid.
Journal of Chemical Theory and Computation, 18:4983-4994,
2022.
|
| 10300. ANARI: A 3-D rendering API standard.
J. E. Stone, K. Griffin, J. Amstutz, D. DeMarle, W. Sherman, and
J. Günther.
Computing in Science and Engineering, 24:7-18, 2022.
|
| 10299. Posttranslational modifications optimize the ability of SARS-CoV-2
spike for effective interaction with host cell receptors.
Karan Kapoor, Tianle Chen, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
119:e2119761119, 2022.
(PMC: PMC9282386) |
| 10297. Experiences porting NAMD to the Data Parallel C++ programming
model.
David J. Hardy, Jaemin Choi, Wei Jiang, and Emad Tajkhorshid.
In International Workshop on OpenCL, IWOCL'22, New York, NY,
USA, 2022. Association for Computing Machinery.
|
| 10298. Extended-ensemble docking to probe dynamic variation of ligand
binding sites during large-scale structural changes of proteins.
Karan Kapoor, Sundar Thangapandian, and Emad Tajkhorshid.
Chemical Science, 13:4150-4169, 2022.
(PMC: PMC8985516) |
| 10290. Role of internal loop dynamics in antibiotic permeability of outer
membrane porins.
Archit Kumar Vasan, Nandan Haloi, Rebecca Joy Ulrich, Mary Elizabeth Metcalf,
Po-Chao Wen, William W. Metcalf, Paul J. Hergenrother, Diwakar Shukla, and
Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
119:e2117009119, 2022.
(PMC: PMC8872756) |
| 10294. Microscopic characterization of the chloride permeation pathway in
the human excitatory amino acid transporter 1 (EAAT1).
Shashank Pant, Qianyi Wu, Renae Ryan, and Emad Tajkhorshid.
ACS Chemical Neuroscience, 13:776-785, 2022.
|
| 10296. Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel
activity and glial regulation of CNS function.
Qianyi Wu, Azman Akhter, Shashank Pant, Eunjoo Cho, Jin Xin Zhu, Alastair R
Garner, Tomoko Ohyama, Emad Tajkhorshid, Donald J van Meyel, and Renae M
Ryan.
Journal of Clinical Investigation, 132:e154891, 2022.
(PMC: PMC8970671) |
| 10295. Use of microscale thermophoresis to measure protein-lipid
interactions.
Robert P. Sparks, William Lawless, Andres S. Arango, Emad Tajkhorshid, and
Rutilio A. Fratti.
Journal of Visualized Experiments, 180, 2022.
|
| 10292. A companion guide to the string method with swarms of trajectories:
Characterization, performance, and pitfalls.
Haochuan Chen, Dylan Ogden, Shashank Pant, Wensheng Cai, Emad Tajkhorshid,
Mahmoud Moradi, Benoit Roux, and Christophe Chipot.
Journal of Chemical Theory and Computation, 18:1406-1422,
2022.
|
| 10293. Identification of structural transitions in bacterial fatty acid
binding proteins that permit ligand entry and exit at membranes.
Jessica M. Gullett, Maxime G. Cuypers, Christy R. Grace, Shashank Pant, Chitra
Subramanian, Emad Tajkhorshid, Charles O. Rock, and Stephen W. White.
Journal of Biological Chemistry, 298:101676, 2022.
(PMC: PMC8892158) |
| 10287. Membrane Mixer: A toolkit for efficient shuffling of lipids in
heterogeneous biological membranes.
Giuseppe Licari, Sepehr Dehghani-Ghahnaviyeh, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 62:986-996,
2022.
|
| 10288. Anionic lipids confine cytochrome c2 to the surface of
bioenergetic membranes without compromising its interaction with redox
partners.
Chun Kit Chan, Abhishek Singharoy, and Emad Tajkhorshid.
Biochemistry, 61:385-397, 2022.
|
| 10289. Anthracycline derivatives inhibit cardiac CYP2J2.
Justin S. Kim, Andres S. Arango, Swapnil Shah, William R Arnold, Emad
Tajkhorshid, and Aditi Das.
Journal of Inorganic Biochemistry, 229:111722, 2022.
(PMC: PMC8860876) |
| 10286. Assembly and analysis of cell-scale membrane envelopes.
Josh Vermaas, Chris Mayne, Eric Shinn, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 62:602-617,
2022.
(PMC: PMC8903035) |
| 10285. Lessons learned from responsive molecular dynamics studies of the
COVID-19 virus.
David J. Hardy, John E. Stone, Barry Isralewitz, and Emad Tajkhorshid.
IEEE/ACM HPC for Urgent Decision Making 2021, pp. 1-10,
2021.
|
| 10284. ChAdOx1 interacts with CAR and PF4 with implications for
thrombosis with thrombocytopenia syndrome.
Alexander T. Baker, Ryan J. Boyd, Daipayan Sarkar, John Vant, Alicia Teijeira
Crespo, Chloe D. Truong, Emily Bates, Eric Wilson, Chun Kit Chan, Magdalena
Lipka-Lloyd, Petra Fromme, Marius Bolni Nagalo, Meike Heurich, Dewight
Williams, Po-Lin Chiu, Pierre J. Rizkallah, Alan L. Parker, Abhishek
Singharoy, and Mitesh J. Borad.
Science Advances, 7:eabl8213, 2021.
|
| 10282. PIP2-dependent coupling of voltage sensor and pore domains in
Kv7.2.
Shashank Pant, Jiaren Zhang, Eung Kim, Kin Lam, Hee Jung Chung, and Emad
Tajkhorshid.
Communications Biology, 4, 2021.
|
| 10281. Rationalizing generation of broad spectrum antibiotics with the
addition of a positive charge.
Nandan Haloi, Archit Kumar Vasan, Emily Jane Geddes, Arjun Prasanna, Po-Chao
Wen, William W. Metcalf, Paul J Hergenrother, and Emad Tajkhorshid.
Chemical Science, 12:15028-15044, 2021.
|
| 10278. CryoFold: Determining protein structures and data-guided ensembles
from cryo-EM density maps.
M. Shekhar, G. Terashi, C. Gupta, D. Sarkar, J. Nguyn, N. J. Sisco, A. Mondal,
J. Vant, P. Fromme, W. D. Van Horn, Emad Tajkhorshid, D. Kihara, K. Dill,
A. Perez, and A. Singharoy.
Matter, 4:3195-3216, 2021.
|
| 10277. Editorial: Mitochondrial exchangers and transporters in cell survival
and death.
Amadou K. S. Camara Wai-Meng Kwok, Emad Tajkhorshid.
Frontiers in Physiology, 12:1415, 2021.
|
| 10311. Differential interactions of selected phytocannabinoids with human
CYP2D6 polymorphisms.
Hannah C. Huff, Archit Vasan, Pritam Roy, Aayush Kaul, Emad Tajkhorshid, and
Aditi Das.
Biochemistry, 60:2749-2760, 2021.
(PMC: PMC8455456) |
| 10280. Molecular mechanism of capsid disassembly in hepatitis B virus.
Zhaleh Ghaemi, Martin Gruebele, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
118:e2102530118, 2021.
|
| 10279. Molecular mechanism of prestin electromotive signal amplification.
Jingpeng Ge, Johannes Elferich, Sepehr Dehghani-Ghahnaviyeh, Zhiyu Zhao, Marc
Meadows, Henrique von Gersdorff, Emad Tajkhorshid, and Eric Gouaux.
Cell, 184:4669-4679, 2021.
|
| 10283. Cryo-EM structures of Escherichia coli cytochrome
bo3 reveal bound phospholipids and ubiquinone-8 in a dynamic
substrate binding site.
Jiao Li, Long Han, Francesca Vallese, Ziqiao Ding, Sylvia K. Choi, Sangjin
Hong, Yanmei Luo, Bin Liu, Chun Kit Chan, Emad Tajkhorshid, Jiapeng Zhu,
Oliver Clarke, Kai Zhang, and Robert Gennis.
Proceedings of the National Academy of Sciences, USA,
118:e2106750118, 2021.
(PMC: PMC8403832) |
| 10265. Amphiphilic distyrylbenzene derivatives as potential therapeutic and
imaging agents for the soluble amyloid-β oligomers in alzheimer's
disease.
Liang Sun, Hong-Jun Cho, Soumyo Sen, Andres S. Arango, Truc T. Huynh, Yiran
Huang, Nilantha Bandara, Buck E. Rogers, Emad Tajkhorshid, and Liviu M.
Mirica.
Journal of the American Chemical Society, 143:10462-10476,
2021.
(PMC: PMC8762579) |
| 10275. Structural basis of complex formation between mitochondrial anion
channel VDAC1 and hexokinase-II.
Nandan Haloi, Po-Chao Wen, Qunli Cheng, Meiying Yang, Gayathri Natarajan,
Amadou KS Camara, Wai-Meng Kwok, and Emad Tajkhorshid.
Communications Biology, 4:667, 2021.
|
| 10276. Defining the energetic basis for a conformational switch mediating
ligand-independent activation of mutant estrogen receptors in breast cancer.
Chris Mayne, W. Toy, K. Carlson, T. Bhatt, S. W. Fanning, G. L. Greene, B. S.
Katzenellenbogen, S. Chandarlapaty, J. A. Katzenellenbogen, and Emad
Tajkhorshid.
Molecular Cancer Research, 19:1559-1570, 2021.
|
| 10274. Calmodulin complexes with brain and muscle creatine kinase peptides.
Janina Sprenger, Anda Trifan, Neal Patel, Ashley Vanderbeck, Jenny Bredtfelt,
Emad Tajkhorshid, Roger Rowlett, Leila Lo Leggio, Karin S. Åkerfeldt, and
Sara Linse.
Current Research in Structural Biology, 3:121-132, 2021.
|
| 10271. Cation-π interactions and their functional roles in membrane
proteins.
Daniel T. Infield, Ali Rasouli, Grace G. Galles, Christophe Chipot, Emad
Tajkhorshid, and Christopher A. Ahern.
Journal of Molecular Biology, 433:167035, 2021.
(PMC: PMC8338773) |
| |
| 10270. Structural insights into photosystem II assembly.
Jure Zabret, Stefan Bohn, Sandra K. Schuller, Oliver Arnolds, Madeline
Möller, Jakob Meier-Credo, Pasqual Liauw, Aaron Chan, Emad Tajkhorshid,
Julian D. Langer, Raphael Stoll, Anja Krieger-Liszkay, Benjamin D. Engel,
Till Rudack, Jan M. Schuller, and Marc M. Nowaczyk.
Nature Plants, 7:524-538, 2021.
|
| 10273. Active participation of membrane lipids in inhibition of multidrug
transporter P-glycoprotein.
Karan Kapoor, Shashank Pant, and Emad Tajkhorshid.
Chemical Science, 12:6293-6306, 2021.
|
| 10269. Multilevel summation for periodic electrostatics using B-splines.
Hüseyin Kaya, David J. Hardy, and Robert D. Skeel.
Journal of Chemical Physics, 154:144105, 2021.
(PMC: PMC8036131) |
| 10268. Classical molecular dynamics.
Charles L. Brooks III, David A. Case, Steve Plimpton, Benoit Roux, David
van der Spoel, and Emad Tajkhorshid.
Journal of Chemical Physics, 154:10041, 2021.
|
| 10264. Glutamate transporters have a chloride channel with two hydrophobic
gates.
Ichia Chen, Shashank Pant, Qianyi Wu, Rosemary Cater, Meghna Sobti, Robert
Vandenberg, Alastair G. Stewart, Emad Tajkhorshid, Josep Font, and Renae
Ryan.
Nature, 591:327-331, 2021.
|
| 10267. Binding mode of SARS-CoV2 fusion peptide to human cellular
membrane.
Defne Gorgun, Muyun Lihan, Karan Kapoor, and Emad Tajkhorshid.
Biophysical Journal, 120:191a, 2021.
|
| 10263. Carbon dioxide transport across membranes.
Marie Michenkova, Sara Taki, Matthew C. Blosser, Hyea J. Hwang, Thomas Kowatz,
Fraser J. Moss, Rossana Occhipinti, Xue Qin, Soumyo Sen, Eric Shinn, Dengke
Wang, Brian S. Zeise, Pan Zhao, Noah Malmstadt, Ardeschir Vahedi-Faridi, Emad
Tajkhorshid, and Walter F. Boron.
Interface Focus, 11:20200090, 2021.
|
| 10266. Mechanical properties of ester- and ether-DPhPC bilayers: a
molecular dynamics study.
Ali Rasouli, Yousef Jamali, Emad Tajkhorshid, Omid Bavi, and Hossein Nejat
Pishkenari.
Journal of the Mechanical Behavior of Biomedical Materials,
117:104386, 2021.
(PMC: PMC8009841) |
| 10260. Anti-inflammatory dopamine- and serotonin-based endocannabinoid
epoxides reciprocally regulate cannabinoid receptors and the TRPV1 channel.
William R. Arnold, Lauren N. Carnevale, Zili Xie, Javier L. Baylon, Emad
Tajkhorshid, Hongzhen Hu, and Aditi Das.
Nature Communications, 12, 2021.
|
| 10261. Multiscale modeling and cinematic visualization of photosynthetic
energy conversion processes from electronic to cell scales.
Melih Sener, Stuart Levy, John E. Stone, AJ Christensen, Barry Isralewitz,
Robert Patterson, Kalina Borkiewicz, Jeffrey Carpenter, C. Neil Hunter, Zaida
Luthey-Schulten, and Donna Cox.
Parallel Computing, 102:102698, 2021.
|
| 10262. Theoretical description of the primary proton-coupled electron
transfer reaction in the cytochrome bc1 complex.
Angela M. Barragan, Alexander V. Soudackov, Zaida Luthey-Schulten, Sharon
Hammes-Schiffer, Klaus Schulten, and Ilia A. Solov'yov.
Journal of the American Chemical Society, 143:715-723, 2021.
|
| 10259. Confronting pitfalls of AI-augmented molecular dynamics using
statistical physics.
Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, and Pratyush
Tiwary.
Journal of Chemical Physics, 153, 2020.
|
| 10255. Hydrogen-deuterium exchange mass spectrometry captures distinct
dynamics upon substrate and inhibitor binding to a transporter.
Ruyu Jia, Chloe Martens, Mrinal Shekhar, Shashank Pant, Grant Pellowe, Andy
Lau, Heather Findlay, Nicola Harris, Emad Tajkhorshid, Paula Booth, and
Argyris Politis.
Nature Communications, 11, 2020.
(PMC: PMC7710758) |
| 10256. The structures of secretory and dimeric immunoglobulin A.
Sonya Kumar Bharathkar, Benjamin W Parker, Andrey G Malyutin, Nandan Haloi,
Kathryn E Huey-Tubman, Emad Tajkhorshid, and Beth Stadtmueller.
eLife, 9:e56098, 2020.
(PMC: PMC7707832) |
| |
| 10254. Parameterization of a drug molecule with a halogen σ-hole
particle using ffTK: Implementation, testing, and comparison.
Yui Tik Pang, Anna Pavlova, Emad Tajkhorshid, and James C. Gumbart.
Journal of Chemical Physics, 153:164104, 2020.
|
| 10251. Membrane surface recognition by the ASAP1 PH domain and
consequences for interactions with the small GTPase Arf1.
O. Soubias, Shashank Pant, F. Heinrich, N. S. Roy Y. Zhang, J. Li, X. Jian,
M. E Yohe, P. A. Randazzo, M. Lösche, Emad Tajkhorshid, and R. A. Byrd.
Science Advances, 6, 2020.
(PMC: PMC7527224) |
| 10250. Structural and functional diversity calls for a new classification of
ABC transporters.
Christoph Thomas, Stephen G. Aller, Konstantinos Beis, Elisabeth P. Carpenter,
Geoffrey Chang, Lei Chen, Elie Dassa, Michel Dean, Franck Duong Van Hoa,
Damian Ekiert, Robert Ford, Rachelle Gaudet, Xin Gong, I. Barry Holland,
Yihua, Vassilis Koronakis, Christopher M. Koth, Youngsook Lee, Oded Lewinson,
Roland Lill, Enrico Martinoia, Satoshi Murakami, Heather W. Pinket, Bert
Poolman, Daniel Rosenbaum, Balazs Sarkadi, Lutz Schmitt, Erwin Schneider,
Yigong Shi, Show-Ling Shyng, Dirk J. Slotboom, Emad Tajkhorshid,
Kazumitsu Ueda D. Peter Tieleman, Andras Varadi, Po-Chao Wen, Nieng Yan, Peng
Zhang, Hongjin Zheng, Jochen Zimmer, and Robert Tampe.
FEBS Letters, 594:3767-3775, 2020.
|
| 10248. Knockout of VDAC1 in H9c2 cells promotes oxidative stress-induced
cell apoptosis through decreased mitochondrial hexokinase II binding and
enhanced glycolytic stress.
Meiying Yang, Jie Sun, David F Stowe, Emad Tajkhorshid, Wai-Meng Kwok, and
Amadou KS Camara.
Cellular Physiology & Biochemistry, 54:853-874, 2020.
Published.
|
| 10253. Structural basis for the reaction cycle of DASS dicarboxylate
transporters.
David B Sauer, Noah Trebesch, Jennifer J Marden, Nicolette Cocco, Jinmei Song,
Akiko Koide, Shohei Koide, Emad Tajkhorshid, and Da-Neng Wang.
eLife, 9:e61350, 2020.
(PMC: PMC7553777) |
| 10258. Scalable analysis of authentic viral envelopes on FRONTERA.
Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla,
and Juan R. Perilla.
Computing in Science and Engineering, 22:11-20, 2020.
|
| 10249. Boosting free-energy perturbation calculations with GPU-accelerated
NAMD.
Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai,
Christophe Chipot, and Emad Tajkhorshid.
Journal of Chemical Information and Modeling, 60:5301-5307,
2020.
(PMC: PMC7686227) |
| 10247. Scalable molecular dynamics on CPU and GPU architectures with
NAMD.
James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone,
João V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin,
Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo,
Brian Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoît Roux,
Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kalé, Klaus
Schulten, Christophe Chipot, and Emad Tajkhorshid.
Journal of Chemical Physics, 153:044130, 2020.
(PMC: PMC7395834) |
| 10246. Aquaporin-7: A dynamic aquaglyceroporin with higher water and
glycerol transport capacity than its bacterial homolog GlpF.
Fraser J Moss, Paween Mahinthichaichan, David T Lodowski, Thomas Kowatz, Emad
Tajkhorshid, Andreas Engel, Walter F Boron, and Ardeshir Vahedi-Faridi.
Frontiers in Physiology, 11, 2020.
Published.
(PMC: PMC7339978) |
| 10244. Aβ(1-42) tetramer and octamer structures reveal edge
conductivity pores as a mechanism for membrane damage.
Sonia Ciudad, Eduard Puig, Thomas Botzanowski, Moeen Meigooni, Andres S.
Arango, Jimmy Do, Maxim Mayzel, Mariam Bayoumi, Stéphane Chaignepain,
Giovanni Maglia, Sarah Cianferani, Vladislav Orekhov, Emad Tajkhorshid,
Benjamin Bardiaux, and Natàlia Carulla.
Nature Communications, 11, 2020.
(PMC: PMC7296003) |
| 10245. Membrane interactions of Cy3/Cy5 fluorophores and their effects on
membrane protein dynamics.
Kin Lam and Emad Tajkhorshid.
Biophysical Journal, 119:24-34, 2020.
(PMC: PMC7335937) |
| 10243. Twisting and tilting of a mechanosensitive molecular probe detects
order in membranes.
Giuseppe Licari, Karolina Strakova, Stefan Matile, and Emad Tajkhorshid.
Chemical Science, 11:5637-5649, 2020.
(PMC: PMC7433777) |
| 10235. A CLC-ec1 mutant reveals global conformational change and suggests
a unifying mechanism for the Cl-/H+ transport cycle.
Tanmay S. Chavan, Ricky C. Cheng, Tao Jiang, Irimpan I. Mathews, Richard A.
Stein, Antoine Koehl, Hassane S. Mchaourab, Emad Tajkhorshid, and Merritt
Maduke.
eLife, 9:e53479, 2020.
(PMC: PMC7253180) |
| 10239. Aberrant expression of a non-muscle RBFOX2 isoform triggers cardiac
conduction defects in myotonic dystrophy.
Chaitali Misra, Sushant Bangru, Feikai Lin, Kin Lam, Sara N. Koenig, Ellen R.
Lubbers, Jamila Hedhli, Nathaniel P. Murphy, Darren J. Parker, Lawrence W.
Dobrucki, Thomas A. Cooper, Emad Tajkhorshid, Peter J. Mohler, and Auinash
Kalsotra.
Developmental Cell, 52:748-763, 2020.
(PMC: PMC7098852) |
| 10241. Menthol binding to the human α4β2 nicotinic
acetylcholine receptor, facilitated by its strong partitioning in membrane.
Rezvan Shahoei and Emad Tajkhorshid.
Journal of Physical Chemistry B, 124:1866-1880, 2020.
(PMC: PMC7094167) |
| 10252. Benchmarking machine learning workloads in structural bioinformatics
applications.
Heng Ma, Austin Clyde, Anda Trifan, Venkatram Vishwanath, Arvind Ramanathan,
Debsindhu Bhowmik, and Shantenu Jha.
First International Workshop on Benchmarking Machine Learning
Workloads on Emerging Hardware: CHALLENGE20, 2020.
|
| 10240. Identifying mutation hotspots reveals pathogenetic mechanisms of
KCNQ2 epileptic encephalopathy.
Jiaren Zhang, Eung Chang Kim, Congcong Chen, Erik Procko, Shashank Pant, Kin
Lam, Jaimin Patel, Rebecca Choi, Mary Hong, Dhruv Joshi, Eric Bolton, Emad
Tajkhorshid, and Hee Jung Chung.
Scientific Reports, 10:4756, 2020.
(PMC: PMC7075958) |
| 10242. Molecular insights into the loading and dynamics of doxorubicin on
PEGylated graphene oxide nanocarriers.
Mina Mahdavi, Ali Fattahi, Emad Tajkhorshid, and Sasan Nouranian.
ACS Applied Bio Materials, 3:1354-1363, 2020.
(PMC: PMC7731932) |
| 10236. Structure and dynamics of the E. coli chemotaxis core
signaling complex by cryo-electron tomography and molecular simulations.
C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S.
Parkinson, Phillip J. Stansfeld, Zaida Luthey-Schulten, and Peijun Zhang.
Communications Biology, 3:24, 2020.
(PMC: PMC6954272) |
| 10237. In situ conformational changes of the Escherichia coli serine
chemoreceptor in different signaling states.
Wen Yang, Keith Cassidy, Peter Ames, Christoph A. Diebolder, Klaus Schulten,
Zaida Luthey-Schulten, John S. Parkinson, and Ariane Briegel.
Molecular Biology and Physiology, 10:e00973-19, 2019.
(PMC: PMC6606802) |
| 10234. Streptavidin/biotin: Tethering geometry defines unbinding mechanics.
Steffen M. Sedlak, Leonard C. Schendel, Hermann E. Gaub, and Rafael C.
Bernardi.
Science Advances, 6:eaay5999, 2020.
|
| 10238. An activity-based sensing approach for the detection of
cyclooxygenase-2 in live cells.
Anuj K. Yadav, Christopher J. Reinhardt, Andres S. Arango, Hannah C. Huff,
Liang Dong, Michael G. Malkowski, Aditi Das, Emad Tajkhorshid, and Jefferson
Chan.
Angewandte Chemie - International Edition in English,
132:2-10, 2019.
|
| 10231. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion
channel embedded in a phosphatidylcholine-only bilayer.
Pramod Kumar, Yuhang Wang, Zhening Zhang, Zhiyu Zhao, Gisela D. Cymes, Emad
Tajkhorshid, and Claudio Grosman.
Proceedings of the National Academy of Sciences, USA,
117:1788-1798, 2020.
(PMC: PMC6983364) |
| 10232. Locking two rigid-body bundles in an outward-facing conformation: A
general ion-coupling mechanism in LeuT-fold transporters.
Jing Li, Zhiyu Zhao, and Emad Tajkhorshid.
Scientific Reports, 9:19479, 2019.
(PMC: PMC6925253) |
| 10218. Computational dissection of membrane transport at a microscopic
level.
Tao Jiang, Po-Chao Wen, Noah Trebesch, Zhiyu Zhao, Shashank Pant, Karan Kapoor,
Mrinal Shekhar, and Emad Tajkhorshid.
Trends in Biochemical Sciences, 45:202-216, 2020.
(PMC: PMC7024014) |
| 10227. Microscopic characterization of GRP1 PH domain interaction with
anionic membranes.
Shashank Pant and Emad Tajkhorshid.
Journal of Computational Chemistry, 41:489-499, 2020.
(PMC: PMC7000246) |
| 10230. Atoms to phenotypes: Molecular design principles of cellular energy
metabolism.
A. Singharoy, C. Maffeo, K. Delgardo, D. J. K. Swainsbury, M. Sener,
U. Kleinekathöfer, B. Isralewitz, I. Teo, D. Chandler, J. Stone,
J. Phillips, T. Pogorelov, M. I. Mallus, C. Chipot, Z. Luthey-Schulten,
P. Tieleman, C. N. Hunter, Emad Tajkhorshid, A. Aksimentiev, and K. Schulten.
Cell, 179:1098-1111, 2019.
|
| 10229. Binding partner- and force-promoted changes in αE-catenin
conformation probed by native cysteine labeling.
Ksenia Terekhova, Sabine Pokutta, Yee S. Kee, Jing Li, Emad Tajkhorshid, Gerald
Fuller, Alexander R. Dunn, and William I. Weis.
Scientific Reports, 9:15375, 2019.
(PMC: PMC6814714) |
| 10228. Federating structural models and data: Outcomes from a workshop on
archiving integrative structures.
Helen M. Berman, Paul D. Adams, Alexandre A. Bonvin, Stephen K. Burley, Bridget
Carragher, Wah Chiu, Frank DiMaio, Thomas E. Ferrin, Margaret J. Gabanyi,
Thomas D. Goddard, Patrick R. Griffin, Juergen Haas, Christian A. Hanke,
Jeffrey C. Hoch, Gerhard Hummer, Genji Kurisu, Catherine L. Lawson, Alexander
Leitner, John L. Markley, Jens Meiler, Gaetano T. Montelione, George
N. Phillips Jr., Thomas Prisner, Juri Rappsilber, David C. Schriemer, Torsten
Schwede, Claus A.M. Seidel, Timothy S. Strutzenberg, Dmitri I. Svergun, Emad
Tajkhorshid, Jill Trewhella, Brinda Vallat, Sameer Velankar, Geerten W.
Vuister, Benjamin Webb, John D. Westbrook, Kate L. White, and Andrej Sali.
Structure, 27:1745-1759, 2019.
|
| 10219. Integrating hydrogen-deuterium exchange mass spectrometry with
molecular dynamics simulations to probe lipid-modulated conformational
changes in membrane proteins.
Chloe Martens, Mrinal Shekhar, Andy M. Lau, Emad Tajkhorshid, and Argyris
Politis.
Nature Protocols, 14:3183-3204, 2019.
Published.
(PMC: PMC7058097) |
| 10225. Tuning symmetry breaking charge separation in perylene bichromophores
by conformational control.
Alexander Aster, Giuseppe Licari, Francesco Zinna, Elodie Brun, Tatu
Kumpulainen, Emad Tajkhorshid, Jerome Lacour, and Eric Vauthey.
Chemical Science, 10:10629-10639, 2019.
|
| 10224. Multivalent polymer-peptide conjugates: A general platform for
inhibiting amyloid beta peptide aggregation.
Xing Jiang, Abigail J. Halmes, Giuseppe Licari, John W. Smith, Yang Song,
Edwin G. Moore, Qian Chen, Emad Tajkhorshid, Chad M. Rienstra, and Jeffrey S.
Moore.
ACS Macro Letters, 8:1365-1371, 2019.
(PMC: PMC7059649) |
| 10222. A chalcogen-bonding cascade switch for planarizable push-pull probes.
Mariano Macchione, Antoine Goujon, Karolina Strakova, Heorhii V. Humeniuk,
Giuseppe Licari, Emad Tajkhorshid, Naomi Sakai, and Stefan Matile.
Angewandte Chemie - International Edition in English,
58:15752-15756, 2019.
(PMC: PMC7035594) |
| 10221. Probing cholesterol binding and translocation in P-glycoprotein.
Sundar Thangapandian, Karan Kapoor, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1862:183090,
2020.
(PMC: PMC6934093) |
| 10220. A small-molecule competitive inhibitor of phosphatidic acid binding
by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole
fusion.
Robert P. Sparks, Andres S. Arango, Matthew L. Starr, Zachary L. Aboff,
Logan R. Hurst, David A. Rivera-Kohr, Chi Zhang, Kevin A. Harden, Jermaine L.
Jenkins, Wayne C. Guida, Emad Tajkhorshid, and Rutilio A. Fratti.
Journal of Biological Chemistry, 294:17168-17185, 2019.
(PMC: PMC6873166) |
| 10226. High-performance analysis of biomolecular containers to measure
small-molecule transport, transbilayer lipid diffusion, and protein cavities.
Alexander J. Bryer, Jodi A. Hadden-Perilla, John E. Stone, and Juan R. Perilla.
Journal of Chemical Information and Modeling, 59:4328-4338,
2019.
(PMC: PMC6817393) |
| 10217. A network of phosphatidylinositol 4,5-bisphosphate binding sites
regulate gating of the Ca2+-activated Cl− channel ANO1
(TMEM16A).
Kuai Yu, Tao Jiang, Yuanyuan Cui, Emad Tajkhorshid, and H Criss Hartzell.
Proceedings of the National Academy of Sciences, USA,
116:19952-19962, 2019.
(PMC: PMC6778221) |
| 10223. Polymer-peptide conjugates convert amyloid into protein nanobundles
through fragmentation and lateral association.
John W. Smith, Xing Jiang, Hyosung An, Alexander M. Barclay, Giuseppe Licari,
Emad Tajkhorshid, Edwin G. Moore, Chad M. Rienstra, Jeffrey S. Moore, and
Qian Shen.
ACS Applied Materials and Interfaces, 3:937-945, 2020.
(PMC: PMC7059651) |
| 10233. Mechanisms of nanonewton mechanostability in a protein complex
revealed by molecular dynamics simulations and single-molecule force
spectroscopy.
Rafael C. Bernardi, Ellis Durner, Constantin Schoeler, Klara H. Malinowska,
Bruna G. Carvalho, Edward A. Bayer, Zaida Luthey-Schulten, Hermann E. Gaub,
and Michael A. Nash.
Journal of the American Chemical Society, 141:14752-14763,
2019.
(PMC: PMC6939381) |
| 10216. Non-syndromic mitral valve dysplasia mutation changes the force
resilience and interaction of human Filamin A.
Tatu J.K. Haataja, Rafael C. Bernardi, Simon Lecointe, Romain Capoulade, Jean
Merot, and Ulla Pentikäinen.
Structure, 27:102-112, 2019.
|
| 10215. Direction matters: Monovalent streptavidin/biotin complex under load.
Steffen M. Sedlak, Leonard C. Schendel, Marcelo C. R. Melo, Diana A. Pippig,
Zaida Luthey-Schulten, Hermann E. Gaub, and Rafael C. Bernardi.
Nano Letters, 19:3415-3421, 2019.
(PMC: PMC6486461) |
| 10214. Structural insights into the lipid A transport pathway in MsbA.
Pius S. Padayatti, Sung Chang Lee, Robyn L. Stanfield, Po-Chao Wen, Emad
Tajkhorshid, Ian A. Wilson, and Qinghai Zhang.
Structure, 27:1114-1123, 2019.
(PMC: PMC6610721) |
| 724. Pro-nifuroxazide self-assembly leads to triggerable nanomedicine for
anti-cancer therapy.
Santosh Misra, Zhe Wu, Fatemeh Ostadhossein, Mao Ye, Kingsley Boateng, Klaus
Schulten, Emad Tajkhorshid, and Dipanjan Pan.
ACS Applied Materials and Interfaces, 11:18074-18089, 2019.
(PMC: PMC7066988) |
| 10213. Serotonin transporter-ibogaine complexes illuminate mechanisms of
inhibition and transport.
Jonathan A. Coleman, Dongxue Yang, Zhiyu Zhao, Po-Chao Wen, Craig Yoshioka,
Emad Tajkhorshid, and Eric Gouaux.
Nature, 569:141-145, 2019.
(PMC: PMC6750207) |
| 10212. Characterization of lipid-protein interactions and lipid-mediated
modulation of membrane protein function through molecular simulations.
Melanie P. Muller, Tao Jiang, Chang Sun, Muyun Lihan, Shashank Pant, Paween
Mahinthichaichan, Anda Trifan, and Emad Tajkhorshid.
Chemical Reviews, 119:6086-6161, 2019.
(PMC: PMC6506392) |
| 723. Fast pressure-jump all-atom simulations and experiments reveal
site-specific protein dehydration-folding dynamics.
Maxim B. Prigozhin, Yi Zhang, Klaus Schulten, Martin Gruebele, and Taras V.
Pogorelov.
Proceedings of the National Academy of Sciences, USA,
116:5356-5361, 2019.
(PMC: PMC6431218) |
| 10211. Allosteric interactions in human cytochrome P450 CYP3A4: The role
of phenylalanine 213.
Ilia G. Denisov, Yelena V. Grinkova, Prithviraj Nandigrami, Mrinal S. Shekhar,
Emad Tajkhorshid, and Stephen G. Sligar.
Biochemistry, 58:1411-1422, 2019.
(PMC: PMC7528618) |
| 10208. Phosphatidic acid induces conformational changes in Sec18 protomers
that prevent SNARE priming.
Matthew L Starr, Robert P Sparks, Andres S Arango, Logan R Hurst, Zhiyu Zhao,
Muyun Lihan, Jermaine L Jenkins, Emad Tajkhorshid, and Rutilio A Fratti.
Journal of Biological Chemistry, 294:3100-3116, 2019.
(PMC: PMC6398130) |
| 10207. Menthol stereoisomers exhibit different effects on α4β2
nAChR upregulation and dopamine neuron spontaneous firing.
Brandon J. Henderson, Stephen Grant, Betty W. Chu, Rezvan Shahoei, Stephanie M.
Huard, Shyam S. M. Saladi, Emad Tajkhorshid, Dennis A. Dougherty, and
Henry A. Lester.
eNeuro, 5:ENEURO.0465-18.2018, 2018.
(PMC: PMC6325563) |
| 10206. Scalable molecular dynamics with NAMD on the Summit system.
Bilge Acun, David J. Hardy, Laxmikant Kale, Ke Li, James C. Phillips, and
John E. Stone.
IBM Journal of Research and Development, 62:4:1-4:9, 2018.
|
| 10210. The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome
acquired hormone resistance in breast cancer cells.
Sean W Fanning, Rinath Jeselsohn, Venkatasubramanian Dharmarajan, Christopher G
Mayne, Mostafa Karimi, Gilles Buchwalter, René Houtman, Weiyi Toy,
Colin E Fowler, Ross Han, Muriel Lainé, Kathryn E Carlson, Teresa A
Martin, Jason Nowak, Jerome C Nwachukwu, David J Hosfield, Sarat
Chandarlapaty, Emad Tajkhorshid, Kendall W Nettles, Patrick R Griffin, Yang
Shen, John A Katzenellenbogen, Myles Brown, and Geoffrey L Greene.
eLife, 7:e37161, 2018.
(PMC: PMC6335054) |
| 10209. Calcium-induced lipid nanocluster structures: Sculpturing of the
plasma membrane.
Michael J. Hallock, Alexander I. Greenwood, Yan Wang, James H. Morrissey, Emad
Tajkhorshid, Chad M. Rienstra, and Taras V. Pogorelov.
Biochemistry, 57:6897-6905, 2018.
(PMC: PMC6475452) |
| 10203. Main-chain mutagenesis reveals intrahelical coupling in an ion
channel voltage-sensor.
Daniel T. Infield, Kimberly Matulef, Jason D. Galpin, Kin Lam, Emad
Tajkhorshid, Christopher A. Ahern, and Francis I. Valiyaveetil.
Nature Communications, 9:5055, 2018.
(PMC: PMC6265297) |
| 10202. Endocannabinoid virodhamine is an endogenous inhibitor of human
cardiovascular CYP2J2 epoxygenase.
Lauren Carnevale, Andres Arango, William R. Arnold, Emad Tajkhorshid, and Aditi
Das.
Biochemistry, 57:6489-6499, 2018.
(PMC: PMC6262108) |
| 10201. Selective permeability of carboxysome shell pores to anionic
molecules.
Paween Mahinthichaichan, Dylan M. Morris, Yi Wang, Grant J. Jensen, and Emad
Tajkhorshid.
Journal of Physical Chemistry B, 122:9110-9118, 2018.
(PMC: PMC6311388) |
| 10200. Direct protein-lipid interactions shape the conformational landscape
of secondary transporters.
C. Martens, M. Shekhar, A. Borysik, A. Lau, E. Reading, E. Tajkhorshid, P. J.
Booth, and A. Politis.
Nature Communications, 9:4151, 2018.
(PMC: PMC6175955) |
| 10204. NanoShaper-VMD interface: computing and visualizing surfaces,
pockets and channels in molecular systems.
Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
Bioinformatics, 35:1241-1243, 2018.
(PMC: PMC6449750) |
| 10199. Constructing atomic structural models into cryo-EM densities using
molecular dynamics - pros and cons.
Yuhang Wang, Mrinal Shekhar, Darren Thifault, Christopher J Williams, Ryan
Mcgreevy, Jane Richardson, Abhishek Singharoy, and Emad Tajkhorshid.
Journal of Structural Biology, 204:319-328, 2018.
(PMC: PMC6394829) |
| 10198. Probing key elements of teixobactin-lipid II interactions in
membrane.
Po-Chao Wen, Juan M Vanegas, Susan B Rempe, and Emad Tajkhorshid.
Chemical Science, 9:6997-7008, 2018.
(PMC: PMC6124899) |
| 10197. Reconstitution and substrate specificity for isopentenyl
pyrophosphate of the antiviral radical SAM enzyme viperin.
Arpita Chakravarti, Kiruthika Selvadurai, Rezvan Shahoei, Hugo Lee, Shirin
Fatma, Emad Tajkhorshid, and Raven H. Huang.
Journal of Biological Chemistry, 293:14122-14133, 2018.
(PMC: PMC6130951) |
| 10193. Electrostatic lock in the transport cycle of the multi-drug
resistance transporter EmrE.
Josh V Vermaas, Susan B. Rempe, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
115:E7502-E7511, 2018.
(PMC: PMC6094130) |
| 10196. Molecular insight into drug exporters within the cellular membrane.
Emad Tajkhorshid.
Pharmacological Research, 133:328, 2018.
|
| 10205. Best practices in running collaborative GPU hackathons: Advancing
scientific applications with a sustained impact.
Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin, Matthew Otten, Dirk
Pleiter, John E Stone, Juan Lucio-Vega, Michael Zingale, and Fernanda
Foertter.
Computing in Science and Engineering, 20:95-106, 2018.
|
| 10195. Microscopic view of lipids and their diverse biological functions.
Po-Chao Wen, Paween Mahinthichaichan, Noah Trebesch, Tao Jiang, Zhiyu Zhao,
Eric Shinn, Mrinal Shekhar Yuhang Wang, Karan Kapoor, Chun Kit Chan, and Emad
Tajkhorshid.
Current Opinion in Structural Biology, 51:177-186, 2018.
(PMC: PMC6221948) |
| 10194. Sensitivity of peripheral membrane proteins to the membrane context:
A case study of phosphatidylserine and the TIM proteins.
Daniel Kerr, Gregory T Tietjen, Zhiliang Gong, Emad Tajkhorshid, Erin J Adams,
and Ka Yee C. Lee.
Biochimica et Biophysica Acta - Biomembranes, 1860:2126-2133,
2018.
(PMC: PMC6290684) |
| 10192. Bacterial denitrifying nitric oxide reductases and aerobic
respiratory terminal oxidases use similar delivery pathways for their
molecular substrates.
Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Bioenergetics, 1859:712-724,
2018.
(PMC: PMC6078787) |
| 10166. CryoEM-based hybrid modeling approaches for structure
determination.
C Keith Cassidy, Benjamin A Himes, Zaida Luthey-Schulten, and Peijun Zhang.
Current Opinion in Microbiology, 43:14-23, 2018.
(PMC: PMC5934336) |
| 10191. Inchworm movement of two rings switching onto a thread by biased
Brownian diffusion represent a three-body problem.
Christopher R. Benson, Christopher Maffeo, Elisabeth M. Fatila, Yun Liu,
Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, and Amar H. Flood.
Proceedings of the National Academy of Sciences, USA,
115:9391-9396, 2018.
(PMC: PMC6156619) |
| 722. All-atom molecular dynamics of the HBV capsid reveals insights into
biological function and cryo-EM resolution limits.
Jodi A Hadden, Juan R Perilla, Christopher John Schlicksup, Balasubramanian
Venkatakrishnan, Adam Zlotnick, and Klaus Schulten.
eLife, 7:e32478, 2018.
(PMC: PMC5927769) |
| 10190. A "cross-stitched" peptide with improved helicity and proteolytic
stability.
Thomas E. Speltz, Christopher G. Mayne, Sean W. Fanning, Zamia Siddiqui, Emad
Tajkhorshid, Geoffrey L Greene, and Terry W. Moore.
Organic & Biomolecular Chemistry, 16:3702-3706, 2018.
(PMC: PMC5993042) |
| 10189. Structural underpinnings of oestrogen receptor mutations in endocrine
therapy resistance.
John A. Katzenellenbogen, Christopher G. Mayne, Benita S. Katzenellenbogen,
Geoffrey L. Greene, and Sarat Chandarlapaty.
Nature Reviews Cancer, 18:377-388, 2018.
(PMC: PMC6252060) |
| 721. Molecular mechanism of extreme mechanostability in a pathogen
adhesin.
Lukas F. Milles, Klaus Schulten, Hermann E. Gaub, and Rafael C. Bernardi.
Science, 359:1527-1533, 2018.
(PMC: PMC6451932) |
| 720. NAMD goes quantum: An integrative suite for hybrid simulations.
Marcelo C. R. Melo, Rafael C. Bernardi, Till Rudack, Maximilian Scheurer,
Christoph Riplinger, James C. Phillips, Julio D. C. Maia, Gerd B. Rocha,
João V. Ribeiro, John E. Stone, Frank Nesse, Klaus Schulten, and Zaida
Luthey-Schulten.
Nature Methods, 15:351-354, 2018.
(PMC: PMC6095686) |
| 10187. Structure of the alternative complex III in a supercomplex with
cytochrome oxidase.
Chang Sun, Samir Benlekbir, Padmaja Venkatakrishnan, Yuhang Wang, Emad
Tajkhorshid, John L. Rubinstein, and Robert B. Gennis.
Nature, 557:123-126, 2018.
(PMC: PMC6004266) |
| 10188. Cytochrome aa3 oxygen reductase utilizes the tunnel
observed in the crystal structures to deliver O2 for catalysis.
Paween Mahinthichaichan, Robert B. Gennis, and Emad Tajkhorshid.
Biochemistry, 57:2150-2161, 2018.
(PMC: PMC5936630) |
| 10186. In situ structure of neuronal C9orf72 poly-GA
aggregates reveals proteasome recruitment.
Qiang Guo, Carina Lehmer, Antonio Martínez-Sánchez, Till Rudack,
Florian Beck, Hannelore Hartmann, Manuela Pérez-Berlanga,
Frédéric Frottin, Mark S. Hipp, F. Ulrich Hartl, Dieter Edbauer,
Wolfgang Baumeister, and Rubén Fernández-Busnadiego.
Cell, 172:696-705, 2018.
(PMC: PMC6035389) |
| 10184. Simulating biological processes: Stochastic physics from whole cells
to colonies.
Tyler Earnest, John Cole, and Zaida Luthey-Schulten.
Reports on Progress in Physics, 81:052601, 2018.
|
| 719. PyContact: Rapid, customizable and visual analysis of non-covalent
interactions in MD simulations.
M. Scheurer, P. Rodenkirch, M. Siggel, R. C. Bernardi, K. Schulten,
E. Tajkhorshid, and T. Rudack.
Biophysical Journal, 114:577-583, 2018.
(PMC: PMC5985026) |
| 10181. Salt bridges gate α-catenin activation at intercellular
junctions.
Samantha Barrick, Jing Li, Xinyu Kong, Alokananda Ray, Emad Tajkhorshid, and
Deborah Leckband.
Molecular Biology of the Cell, 29:111-122, 2018.
(PMC: PMC5909925) |
| 10179. Arachidonic acid metabolism by human cardiovascular CYP2J2 is
modulated by doxorubicin.
William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das.
Biochemistry, 56:6700-6712, 2017.
(PMC: PMC5743546) |
| 10180. Drug-drug interactions between atorvastatin and dronedarone mediated
by monomeric CYP3A4.
Ilia G. Denisov, Javier L. Baylon, Yelena V. Grinkova, Emad Tajkhorshid, and
Stephen G. Sligar.
Biochemistry, 57:805-816, 2017.
(PMC: PMC5800941) |
| 717. Quenching protein dynamics interferes with HIV capsid maturation.
Mingzhang Wang, Caitlin M. Quinn, Juan R. Perilla, Huilan Zhang, Randall Shirra
Jr., Guangjin Hou, In-Ja Byeon, Christopher L. Suiter, Sherimay Ablan, Emiko
Urano, Theodore J. Nitz, Christopher Aiken, Eric O. Freed, Peijun Zhang,
Klaus Schulten, Angela M. Gronenborn, and Tatyana Polenova.
Nature Communications, 8:1779, 2017.
(PMC: PMC5701193) |
| 10175. Porphyrin-assisted docking of a thermophage portal protein into lipid
bilayers: Nanopore engineering and characterization.
Benjamin Cressiot, Sandra J. Greive, Wei Si, Tomas C. Pascoa, Mehrnaz
Mojtabavi, Maria Chechik, Huw T. Jenkins, Xueguang Lu, Ke Zhang, Aleksei
Aksimentiev, Alfred A. Antson, and Meni Wanunu.
ACS Nano, 11:11931-11945, 2017.
(PMC: PMC5963890) |
| 716. Constant-pH molecular dynamics simulations for large biomolecular
systems.
Brian K. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang,
James C. Phillips, Klaus Schulten, and Benoît Roux.
Journal of Chemical Theory and Computation, 13:5933-5944,
2017.
(PMC: PMC5726918) |
| 10162. Chasing the open-state structure of pentameric ligand-gated ion
channels.
Giovanni Gonzalez-Gutierrez, Yuhang Wang, Gisela Cymes, Emad Tajkhorshid, and
Claudio Grosman.
Journal of General Physiology, 149:1119-1138, 2017.
(PMC: PMC5715906) |
| 10174. Quantification of membrane protein-detergent complex interactions.
Aaron J. Wolfe, Wei Si, Zhengqi Zhang, Adam R. Blanden, Yi-Ching Hsueh, Jack F.
Gugel, Bach Pham, Min Chen, Stewart N. Loh, Sharon Rozovsky, Aleksei
Aksimentiev, and Liviu Movileanu.
Journal of Physical Chemistry B, 121:10228-10241, 2017.
(PMC: PMC5680101) |
| 10163. Lipids and ions traverse the membrane by the same physical pathway in
the nhTMEM16 scramblase.
Tao Jiang, Kuai Yu, H. Criss Hartzell, and Emad Tajkhorshid.
eLife, 6:e28671, 2017.
(PMC: PMC5628016) |
| 10161. Combining in Vitro and in Silico single molecule force
spectroscopy to characterize and tune cellulosomal scaffoldin mechanics.
Tobias Verdorfer, Rafael C. Bernardi, Aylin Meinhold, Wolfgang Ott, Zaida
Luthey-Schulten, Michael A. Nash, and Hermann E. Gaub.
Journal of the American Chemical Society, 139:17841-17852,
2017.
(PMC: PMC5737924) |
| 10160. Coupling X-ray reflectivity and in silico binding to yield dynamics
of membrane recognition by Tim1.
Gregory T. Tietjen, Javier L. Baylon, Daniel Kerr, Zhiliang Gong, J. Michael
Henderson, Charles T. R. Heffern, Mati Meron, Binhua Lin, Mark L. Schlossman,
Erin J. Adams, Emad Tajkhorshid, and Ka Yee C. Lee.
Biophysical Journal, 113:1505-1519, 2017.
(PMC: PMC5627149) |
| 715. CryoEM structure of MxB reveals a novel oligomerization interface
critical for HIV restriction.
Frances J. D. Alvarez, Shaoda He, Juan R. Perilla, Sooin Jang, Klaus Schulten,
Alan N. Engelman, Sjors H. W. Scheres, and Peijun Zhang.
Science Advances, 3:e1701264, 2017.
(PMC: PMC5600524) |
| 10183. Population FBA predicts metabolic phenotypes in yeast.
Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, and Zaida Luthey-Schulten.
PLoS Computational Biology, 13:e1005728, 2017.
(PMC: PMC5626512) |
| 10164. Activation and desensitization mechanism of AMPA receptor-tarp
complex by cryo-EM.
Shanshuang Chen, Yan Zhao, Yuhang Wang, Mrinal Shekhar, Emad Tajkhorshid, and
Eric Gouaux.
Cell, 170:1234-1246, 2017.
(PMC: PMC5621841) |
| 714. Detection of methylation on dsDNA using nanopores in a MoS2
membrane.
Jiwook Shim, Shouvik Banerjee, Hu Qiu, Kirby K. H. Smithe, David Estrada,
Julian Bello, Eric Pop, Klaus Schulten, and Rashid Bashir.
Nanoscale, 9:14836-14845, 2017.
|
| 10177. Parametric studies of metabolic cooperativity in escherichia coli
colonies: Strain and geometric confinement effects.
Joseph R. Peterson, John A. Cole, and Zaida Luthey-Schulten.
PLoS One, 12:e0182570, 2017.
(PMC: PMC5562313) |
| 10158. Lipid specificity of the membrane binding domain of coagulation
factor X.
Melanie P. Muller, Yan Wang, James H. Morrissey, and Emad Tajkhorshid.
Journal of Thrombosis and Haemostasis, 15:2005-2016, 2017.
(PMC: PMC5630516) |
| 10182. Nanoscale ion pump derived from a biological water channel.
Karl Decker, Martin Page, and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:7899-7906, 2017.
(PMC: PMC5570624) |
| 712. Physical properties of the HIV-1 capsid from all-atom molecular
dynamics simulations.
Juan R. Perilla and Klaus Schulten.
Nature Communications, 8:15959, 2017.
(PMC: PMC5524983) |
| 10176. Careful accounting of extrinsic noise in protein expression reveals
correlations among its sources.
John A. Cole and Zaida Luthey-Schulten.
Physical Review E, 95:062418, 2017.
(PMC: PMC5669626) |
| 711. Skeletal dysplasia mutations effect on human filamins' structure and
mechanosensing.
Jonne Seppälä, Rafael C. Bernardi, Tatu J. K. Haataja, Maarit Hellman,
Olli T. Pentikäinen, Klaus Schulten, Perttu Permi, Jari Ylänne, and
Ulla Pentikäinen.
Scientific Reports, 7:4218, 2017.
(PMC: PMC5484675) |
| 10157. Critical role of water molecules in proton translocation by the
membrane-bound transhydrogenase.
Pius S. Padayatti, Josephine H. Leung, Paween Mahinthichaichan, Emad
Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S. Michael Soltis, J. Baz
Jackson, C. David Stout, Robert B. Gennis, and Qinghai Zhang.
Structure, 25:1111-1119, 2017.
(PMC: PMC5524145) |
| 718. Lateral segregation of Photosystem I in cyanobacterial
thylakoid.
Craig MacGregor-Chatwin, Melih Sener, Samuel F.H. Barnett, Andrew Hitchcock,
Meghan C. Barnhart-Dailey, Karim Maghlaoui, James Barber, Jerilyn A. Timlin,
Klaus Schulten, and C. Neil Hunter.
Plant Cell, 29:1119-1136, 2017.
(PMC: PMC5466035) |
| 10173. Dimeric structure of the uracil: proton symporter UraA provides
mechanistic insights into the SLC4/23/26 transporters.
Xinzhe Yu, Guanghui Yang, Chuangye Yan, Javier L Baylon, Jing Jiang, He Fan,
Guifeng Lu, Kazuya Hasegawa, Hideo Okumura, Tingliang Wang, Emad Tajkhorshid,
Shuo Li, and Nieng Yan.
Cell Research, 27:1020-1033, 2017.
(PMC: PMC5539350) |
| 710. Angular measurements of the dynein ring reveal a stepping mechanism
dependent on a flexible stalk.
Lisa G. Lippert, Tali Dadosh, Jodi A. Hadden, Benjamin T. Diroll,
Christopher B. Murray, Erika L.F. Holzbaur, Klaus Schulten, Samara L.
Reck-Peterson, and Yale E. Goldman.
Proceedings of the National Academy of Sciences, USA,
114:E4564-E4573, 2017.
(PMC: PMC5468668) |
| 713. Permeability of a fluid lipid bilayer to short-chain alcohols from
first principles.
Jeffrey Comer, Klaus Schulten, and Christophe Chipot.
Journal of Chemical Theory and Computation, 13:2523-2532,
2017.
|
| 10178. CryoEM structure refinement by integrating NMR chemical shifts
with molecular dynamics simulations.
Juan R. Perilla, Gongpu Zhao, Manman Lu, Jiying Ning, Guangjin Hou, In-Ja L.
Byeon, Angela M. Gronenborn, Tatyana Polenova, and Peijun Zhang.
Journal of Physical Chemistry B, 121:3853-3863, 2017.
(PMC: PMC5459578) |
| 10172. Determination of cell doubling times from the return-on-investment
time of photosynthetic vesicles based on atomic detail structural models.
Andrew Hitchcock, C. Neil Hunter, and Melih Sener.
Journal of Physical Chemistry B, 121:3787-3797, 2017.
|
| 10152. Tribute to Klaus Schulten.
Emad Tajkhorshid and Christophe Chipot.
Journal of Physical Chemistry B, 121:3203-3205, 2017.
|
| 10151. A membrane-embedded pathway delivers general anesthetics to two
interacting binding sites in the Gloeobacter violaceus ion channel.
Mark J Arcario, Christopher G Mayne, and Emad Tajkhorshid.
Journal of Biological Chemistry, 9:9480-9492, 2017.
(PMC: PMC5465477) |
| 708. Detection and mapping of DNA methylation with 2D material
nanopores.
Hu Qiu, Aditya Sarathy, Klaus Schulten, and Jean-Pierre Leburton.
npj 2D Materials and Applications, 1:3, 2017.
(PMC: PMC5794036) |
| 10155. Challenges of integrating stochastic dynamics and cryo-electron
tomograms in whole-cell simulations.
Tyler M. Earnest, Reika Watanabe, John E. Stone, Julia Mahamid, Wolfgang
Baumeister, Elizabeth Villa, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 121:3871-3881, 2017.
|
| 10150. Energy transduction and alternating access of the mammalian ABC
transporter P-glycoprotein.
Brandy Verhalen, Reza Dastvan, Sundarapandian Thangapandian, Yelena Peskova,
Hanane A. Koteiche, Robert K. Nakamoto, Emad Tajkhorshid, and Hassane S.
Mchaourab.
Nature, 543:738-741, 2017.
(PMC: PMC5558441) |
| 707. Quantitative characterization of domain motions in molecular
machines.
Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, and Joachim Frank.
Journal of Physical Chemistry B, 121:3747-3756, 2017.
(PMC: PMC5479934) |
| 10154. Extension of the highly mobile membrane mimetic to transmembrane
systems through customized in Silico solvents.
Josh V. Vermaas, Taras V. Pogorelov, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 121:3764-3776, 2017.
|
| 10165. Mitochondrial VDAC1: A key gatekeeper as potential therapeutic
target.
Amadou K.S. Camara, Yi Fan Zhou, Po Chao Wen, Emad Tajkhorshid, and Wai Meng
Kwok.
Frontiers in Physiology, 8:640, 2017.
(PMC: PMC5491678) |
| 10149. Mass spectrometry-based cross-linking study shows that the Psb28
protein binds to cytochrome b559 in Photosystem II.
Daniel A. Weisz, Haijun Liu, Hao Zhang, Sundarapandian Thangapandian, Emad
Tajkhorshid, Michael L. Gross, and Himadri B. Pakrasi.
Proceedings of the National Academy of Sciences, USA,
114:2224-2229, 2017.
(PMC: PMC5338524) |
| 10147. Differential membrane binding mechanics of synaptotagmin isoforms
observed at atomic detail.
Josh V. Vermaas and Emad Tajkhorshid.
Biochemistry, 56:281-293, 2017.
(PMC: PMC5557660) |
| 10148. Structural basis of co-translational quality control by ArfA and
RF2 bound to ribosome.
Fuxing Zeng, Yanbo Chen, Jonathan Remis, Mrinal Shekhar, James C. Phillips,
Emad Tajkhorshid, and Hong Jin.
Nature, 541:554-557, 2017.
(PMC: PMC5679781) |
| 706. Structural insights into the functional cycle of the ATPase module
of the 26S proteasome.
Marc Wehmer, Till Rudack, Florian Beck, Antje Aufderheide, Günter Pfeifer,
Jürgen M. Plitzko, Friedrich Förster, Klaus Schulten, Wolfgang
Baumeister, and Eri Sakata.
Proceedings of the National Academy of Sciences, USA,
114:1305-1310, 2017.
(PMC: PMC5307450) |
| 709. Computational de novo design of antibodies binding to a peptide with
high affinity.
Venkata Giridhar Poosarla, Tong Li, Boon Chong Goh, Klaus Schulten, Thomas K.
Wood, and Costas D. Maranas.
Biotechnology and Bioengineering, 114:1331-1342, 2017.
(PMC: PMC5726764) |
| 10153. Modulation of molecular flux using a graphene nanopore capacitor.
Manish Shankla and Aleksei Aksimentiev.
Journal of Physical Chemistry B, 121:3724-3733, 2016.
|
| 705. CHRAMM-GUI MDFF/xMDFF utilizer for molecular dynamics flexible
fitting simulations in various environments.
Yifei Qi, Jumin Lee, Abhishek Singharoy, Ryan Mcgreevy, Klaus Schulten, and
Wonpil Im.
Journal of Physical Chemistry B, 121:3718-3723, 2016.
(PMC: PMC5398930) |
| 703. Chemomechanical coupling in hexameric protein-protein interfaces
harnesses energy within V-type ATPases.
Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, and Klaus Schulten.
Journal of the American Chemical Society, 139:293-310, 2017.
(PMC: PMC5518570) |
| 10156. Computational characterization of molecular mechanisms of membrane
transporter function.
Noah Trebesch, Josh V. Vermaas, and Emad Tajkhorshid.
In Carmen Domene, editor, Computational Biophysics of Membrane
Proteins, chapter 7, pp. 197-236. Royal Society of Chemistry, Cambridge,
UK, 2017.
|
| 704. A central cavity within the holo-translocon suggests a mechanism for
membrane protein insertion.
Mathieu Botte, Nathan Zaccai, Jelger Lycklama à Nijeholt, Remy Martin,
Kèvin Knoops, Gabor Papai, Juan Zou, Aurélien Deniaud, Manikandan
Karuppasamy, Qiyang Jiang, Abhishek Singha Roy, Klaus Schulten, Patrick
Schultz, Juri Rappsilber, Giuseppe Zaccai, Imre Berger, Ian Collinson, and
Christiane Schaffitzel.
Scientific Reports, 6:38399, 2016.
(PMC: PMC5141469) |
| 10144. Asymmetric binding and metabolism of polyunsaturated fatty acids
(PUFAs) by CYP2J2 epoxygenase.
William R. Arnold, Javier L. Baylon, Emad Tajkhorshid, and Aditi Das.
Biochemistry, 55:6969-6980, 2016.
(PMC: PMC5558443) |
| 10145. Genome-wide gene expression and RNA half-life measurements allow
predictions of regulation and metabolic behavior in Methanosarcina
acetivorans.
Joseph R Peterson, ShengShee Thor, Lars Kohler, Petra RA Kohler, William W
Metcalf, and Zaida Luthey-Schulten.
BMC Genomics, 17:924, 2016.
(PMC: PMC5112694) |
| 10146. Methodology for the simulation of molecular motors at different
scales.
Abhishek Singharoy and Christophe Chipot.
Journal of Physical Chemistry B, 121:3502-3514, 2017.
(PMC: PMC5518690) |
| 702. HIV-1 capsid function is regulated by dynamics: Quantitative
atomic-resolution insights by integrating magic-angle-spinning NMR,
QM/MM, and MD.
Huilan Zhang, Guangjin Hou, Manman Lu, Jinwoo Ahn, In-Ja L. Byeon,
Christopher J. Langmead, Juan R. Perilla, Ivan Hung, Peter L. Gor'kov,
Zhehong Gan, William W. Brey, David A. Case, Klaus Schulten, Angela M.
Gronenborn, and Tatyana Polenova.
Journal of the American Chemical Society, 138:14066-14075,
2016.
(PMC: PMC5380593) |
| 701. Crystal structure and conformational change mechanism of a bacterial
Nramp-family divalent metal transporter.
Aaron T. Bozzi, Lukas B. Bane, Wilhelm A. Weihofen, Abhishek Singharoy,
Eduardo R. Guillen, Hidde L. Ploegh, Klaus Schulten, and Rachelle Gaudet.
Structure, 24:2102-2114, 2016.
(PMC: PMC5143219) |
| 700. Mechanism of the primary charge transfer reaction in the cytochrome
bc1 complex.
Angela M. Barragan, Klaus Schulten, and Ilia A. Solov'yov.
Journal of Physical Chemistry B, 120:11369-11380, 2016.
|
| 10159. X-ray structures define human P2X3 receptor gating cycle and
antagonist action.
Steven E. Mansoor, Wei Lü, Wout Oosterheert, Mrinal Shekhar, Emad
Tajkhorshid, and Eric Gouaux.
Nature, 538:66-71, 2016.
(PMC: PMC5161641) |
| 10171. Q-band electron-nuclear double resonance reveals out-of-plane
hydrogen bonds stabilize an anionic ubisemiquinone in cytochrome bo3 from
Escherichia coli.
Chang Sun, Alexander T. Taguchi, Josh V. Vermaas, Nathan J. Beal, Patrick J.
O'Malley, Emad Tajkhorshid, Robert B. Gennis, and Sergei A. Dikanov.
Biochemistry, 55:5714-5725, 2016.
(PMC: PMC5558440) |
| 699. 3D implementation of the symbol nomenclature for graphical
representation of glycans.
David F. Thieker, Jodi A. Hadden, Klaus Schulten, and Robert J. Woods.
Glycobiology, 26:786-787, 2016.
(PMC: PMC5018049) |
| 698. Binding site recognition and docking dynamics of a single electron
transport protein: Cytochrome c2.
Abhishek Singharoy, Angela M. Barragan, Sundarapandian Thangapandian, Emad
Tajkhorshid, and Klaus Schulten.
Journal of the American Chemical Society, 138:12077-12089,
2016.
(PMC: PMC5518707) |
| 10143. Large-conductance transmembrane porin made from DNA origami.
Kerstin Göpfrich, Chen-Yu Li, Maria Ricci, Satya Prathyusha Bhamidimarri,
Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei
Aksimentiev, and Ulrich F. Keyser.
ACS Nano, 10:8207-8214, 2016.
|
| 697. Conserved methionine dictates substrate preference in Nramp-family
divalent metal transporters.
Aaron T. Bozzi, Lukas B. Bane, Wilhelm Weihofen, Anne McCabe, Abhishek
Singharoy, Chris Chipot, Klaus Schulten, and Rachelle Gaudet.
Proceedings of the National Academy of Sciences, USA,
113:10310-10315, 2016.
(PMC: PMC5027461) |
| 10169. Ribosome biogenesis in replicating cells: integration of experiment
and theory.
Tyler M. Earnest, John A. Cole, Joseph R. Peterson, Michael J. Hallock,
Thomas E. Kuhlman, and Zaida Luthey-Schulten.
Biopolymers, 105:735-751, 2016.
(PMC: PMC4958520) |
| 696. Overall energy conversion efficiency of a photosynthetic vesicle.
Melih Sener, Johan Strümpfer, Abhishek Singharoy, C. Neil Hunter, and Klaus
Schulten.
eLife, 10.7554/eLife.09541, 2016.
(30 pages).
(PMC: PMC5001839) |
| 695. Molecular dynamics-based refinement and validation for sub-5 Å
cryo-electron microscopy maps.
Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and
Klaus Schulten.
eLife, 10.7554/eLife.16105, 2016.
(PMC: PMC4990421) |
| 694. The structure of the human 26S proteasome at a resolution of 3.9
Å.
Andreas Schweitzer, Antje Aufderheide, Till Rudack, Florian Beck, Gunter
Pfeifer, Jurgen M. Plitzko, Eri Sakata, Klaus Schulten, Friedrich Forster,
and Wolfgang Baumeister.
Proceedings of the National Academy of Sciences, USA,
113:7816-7821, 2016.
(PMC: PMC4948313) |
| 10142. Ion channels made from a single membrane-spanning DNA duplex.
Kerstin Göpfrich, Chen-Yu Li, Iwona Mames, Satya Prathyusha Bhamidimarri,
Maria Ricci, Jejoong Yoo, Adam Mames, Alexander Ohmann, Mathias Winterhalter,
Eugen Stulz, Aleksei Aksimentiev, and Ulrich F. Keyser.
Nano Letters, 16:4665-4669, 2016.
(PMC: PMC4948918) |
| 693. Dynamic behavior of trigger factor on the ribosome.
Julian Deeng, Kwok-Yan Chan, Eli O. van der Sluis, Lukas Bischoff, Otto
Berninghausen, Wei Han, James Gumbart, Klaus Schulten, Birgitta Beatrix, and
Roland Beckmann.
Journal of Molecular Biology, 428:3588-3602, 2016.
|
| 692. A time-course of orchestrated endophilin action in sensing, bending,
and stabilizing curved membranes.
Kumud R Poudel, Yongming Dong, Hang Yu, Allen Su, Thuong Ho, Yan Liu, Klaus
Schulten, and Jihong Bai.
Molecular Biology of the Cell, 27:2119-2132, 2016.
(PMC: PMC4927284) |
| 10167. TopoGromacs: Automated topology conversion from CHARMM to
GROMACS within VMD.
Josh V. Vermaas, David J. Hardy, John E. Stone, Emad Tajkhorshid, and Axel
Kohlmeyer.
Journal of Chemical Information and Modeling, 56:1112-1116,
2016.
|
| 691. Elucidation of lipid binding sites on lung surfactant protein A
using X-ray crystallography, mutagenesis and molecular dynamics
simulations.
Boon Chong Goh, Huixing Wu, Michael J. Rynkiewicz, Klaus Schulten, Barbara A.
Seaton, and Francis X. McCormack.
Biochemistry, 55:3692-3701, 2016.
(PMC: PMC5663190) |
| 690. Early experiences porting the NAMD and VMD molecular simulation
and analysis software to GPU-accelerated OpenPOWER platforms.
John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
International Workshop on OpenPOWER for HPC (IWOPH'16), pp.
188-206, 2016.
|
| 689. The water permeability and pore entrance structure of aquaporin-4
channels depend on lipid bilayer thickness.
Jihong Tong, Zhe Wu, Margaret M. Briggs, Klaus Schulten, and Thomas J.
Mclntosh.
Biophysical Journal, 111:90-99, 2016.
(PMC: PMC4944661) |
| 688. Adaptive multilevel splitting method for molecular dynamics
calculation of benzamidine-trypsin dissociation time.
Ivan Teo, Christopher G. Mayne, Klaus Schulten, and Tony Lelievre.
Journal of Chemical Theory and Computation, 12:2983-2989,
2016.
|
| 10115. The cellular membrane as a mediator for small molecule interaction
with membrane proteins.
Christopher G. Mayne, Mark J. Arcario, Paween Mahinthichaichan, Javier L.
Baylon, Josh V. Vermaas, Latifeh Navidpour, Po-Chao Wen, Sundarapandian
Thangapandian, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1858:2290-2304,
2016.
(PMC: PMC4983535) |
| 687. QwikMD-integrative molecular dynamics toolkit for novices and
experts.
Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C.
Phillips, Peter L. Freddolino, and Klaus Schulten.
Scientific Reports, 6:26536, 2016.
(PMC: PMC4877583) |
| 686. All-atom molecular dynamics of virus capsids as drug targets.
Juan R. Perilla, Jodi A. Hadden, Boon Chong Goh, Christopher G. Mayne, and
Klaus Schulten.
Journal of Physical Chemistry Letters, 7:1836-1844, 2016.
(PMC: PMC4876486) |
| 10125. Molecular architecture of the retroviral capsid.
Juan R Perilla and Angela M Gronenborn.
Trends in Biochemical Sciences, 41:410-420, 2016.
(PMC: PMC4879823) |
| 685. Contributions of charged residues in structurally dynamic capsid
surface loops to Rous sarcoma virus assembly.
Katrina Heyrana, Boon Chong Goh, Juan Roberto Perilla, Tam-Linh N. Nguyen,
Matthew R. England, Maria C. Bewley, Klaus Schulten, and Rebecca Craven.
Journal of Virology, 90:5700-5714, 2016.
(PMC: PMC4886791) |
| 684. Flexibility coexists with shape persistence in cyanostar macrocycles.
Yun Liu, Abhishek Singharoy, Christopher G. Mayne, Arkajyoti Sengupta, Krishnan
Raghavachari, Klaus Schulten, and Amar H. Flood.
Journal of the American Chemical Society, 138:4843-4851, 2016.
(PMC: PMC4957974) |
| 683. Recognition of poly-ubiquitins by the proteasome through protein
re-folding guided by electrostatic and hydrophobic interactions.
Yi Zhang, Lela Vukovic, Till Rudack, Wei Han, and Klaus Schulten.
Journal of Physical Chemistry B, 120:8137-8146, 2016.
(PMC: PMC5001906) |
| 682. Disulfide bridges: bringing together frustrated structure in a
bioactive peptide.
Yi Zhang, Klaus Schulten, Martin Gruebele, Paramjit S. Bansal, David Wilson,
and Norelle L. Daly.
Biophysical Journal, 110:1744-1752, 2016.
(PMC: PMC4850350) |
| 681. Electrically tunable quenching of DNA fluctuations in biased
solid-state nanopores.
Hu Qiu, Anuj Girdhar, Klaus Schulten, and Jean-Pierre Leburton.
ACS Nano, 10:4482-4488, 2016.
(PMC: PMC4918906) |
| 10128. Direct evidence for sequence-dependent attraction between
double-stranded DNA controlled by methylation.
Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev, and Taekjip Ha.
Nature Communications, 7:11045, 2016.
(PMC: PMC4804163) |
| 677. Multilevel summation with B-spline interpolation for pairwise
interactions in molecular dynamics simulations.
David J. Hardy, Matthew A. Wolff, Jianlin Xia, Klaus Schulten, and Robert D.
Skeel.
Journal of Chemical Physics, 144:114112, 2016.
(16 pages).
(PMC: PMC4808071) |
| 10113. Stapled peptides with γ-methylated hydrocarbon chains for
the estrogen receptor/coactivator interaction.
Thomas E. Speltz, Sean W. Fanning, Christopher G. Mayne, Colin Fowler, Emad
Tajkhorshid, Geoffrey L. Greene, and Terry W. Moore.
Angewandte Chemie - International Edition in English,
55:4252-4255, 2016.
|
| 678. Immersive molecular visualization with omnidirectional stereoscopic
ray tracing and remote rendering.
John E. Stone, William R. Sherman, and Klaus Schulten.
2016 IEEE International Parallel and Distributed Processing
Symposium Workshop (IPDPSW), pp. 1048-1057, 2016.
(PMC: PMC5063251) |
| 679. High performance molecular visualization: In-situ and parallel
rendering with EGL.
John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten.
2016 IEEE International Parallel and Distributed Processing
Symposium Workshop (IPDPSW), pp. 1014-1023, 2016.
(PMC: PMC5061511) |
| 680. Evaluation of emerging energy-efficient heterogeneous computing
platforms for biomolecular and cellular simulation workloads.
John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida
Luthey-Schulten, and Klaus Schulten.
2016 IEEE International Parallel and Distributed Processing
Symposium Workshop (IPDPSW), pp. 89-100, 2016.
(PMC: PMC4978513) |
| 10168. Conformational dynamics of the human islet amyloid polypeptide in a
membrane environment: Toward the aggregation prone form.
Katrine Kirkeby Skeby, Ole Juul Andersen, Taras V. Pogorelov, Emad Tajkhorshid,
and Birgit Schiott.
Biochemistry, 55:2031-2042, 2016.
|
| 676. Cyclophilin A stabilizes HIV-1 capsid through a novel
non-canonical binding site.
Chuang Liu, Juan R. Perilla, Jiying Ning, Manman Lu, Guangjin Hou, Ruben
Ramalho, Gregory Bedwell, In-Ja Byeon, Jinwoo Ahn, Jiong Shi, Angela
Gronenborn, Peter Prevelige, Itay Rousso, Christopher Aiken, Tatyana
Polenova, Klaus Schulten, and Peijun Zhang.
Nature Communications, 7:10714, 2016.
(PMC: PMC4785225) |
| 10170. Atomic-level description of protein-lipid interactions using an
accelerated membrane model.
Javier L. Baylon, Josh V. Vermaas, Melanie P. Muller, Mark J. Arcario, Taras V.
Pogorelov, and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1858:1573-1583,
2016.
(PMC: PMC4877275) |
| 675. Molecular mechanism of processive 3' to 5' RNA translocation in the
active subunit of the RNA exosome complex.
Lela Vukovic, Christophe Chipot, Debora L. Makino, Elena Conti, and Klaus
Schulten.
Journal of the American Chemical Society, 138:4069-4078, 2016.
(PMC: PMC4988868) |
| 10185. Effects of cytosine modifications on DNA flexibility and nucleosome
mechanical stability.
Thuy TM Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei
Aksimentiev, and Taekjip Ha.
Nature Communications, 7:10813, 2016.
(PMC: PMC4770088) |
| 10111. All the O2 consumed by Thermus thermophilus
cytochrome ba3 is delivered to the active site through a long,
open hydrophobic tunnel with entrances within the lipid bilayer.
Paween Mahinthichaichan, Robert Gennis, and Emad Tajkhorshid.
Biochemistry, 55:1265-1278, 2016.
(PMC: PMC5142635) |
| 10114. Enhancing Mn(II)-binding and manganese peroxidase activity in a
designed cytochrome c peroxidase through fine-tuning secondary-sphere
interactions.
Parisa Hosseinzadeh, Evan N. Mirts, Thomas D. Pfister, Yi-Gui Gao, Christopher
Mayne, Howard Robinson, Emad Tajkhorshid, and Yi Lu.
Biochemistry, 55:1494-1502, 2016.
|
| 10110. Revealing an outward-facing open conformational state in a CLC
Cl/H exchange transporter.
Chandra M Khantwal, Sherwin J Abraham, Wei Han, Tao Jiang, Tanmay S Chavan,
Ricky C Cheng, Shelley M Elvington, Corey W Liu, Irimpan I Mathews, Richard A
Stein, Hassane S Mchaourab, Emad Tajkhorshid, and Merritt Maduke.
eLife, 5:e11189, 2016.
(PMC: PMC4769167) |
| 10112. Molecular basis for differential anion binding and proton coupling in
the Cl−/H+ exchanger ClC-ec1.
Tao Jiang, Wei Han, Merritt Maduke, and Emad Tajkhorshid.
Journal of the American Chemical Society, 138:3066-3075, 2016.
|
| 10127. The structure and intermolecular forces of DNA condensates.
Jejoong Yoo and Aleksei Aksimentiev.
Nucleic Acids Research, 44:2036-2046, 2016.
(PMC: PMC4797306) |
| 10109. Estrogen receptor alpha somatic mutations Y537S and D538G confer
breast cancer endocrine resistance by stabilizing the activating function-2
binding conformation.
Sean W Fanning, Christopher G Mayne, Venkatasubramanjan Dharmarajan, Kathryn E
Carlson, Teresa A Martin, Scott J Novick, Weiyi Toy, Bradley Green, Srinivas
Panchamukhi, Benita S Katzenellenbogen, Emad Tajkhorshid, Patrick R Griffin,
Yang Shen, Sarat Chandarlapaty, John A Katzenellenbogen, and Geoffrey L
Greene.
eLife, pp. e12792, 2016.
(PMC: PMC4821807) |
| 674. Computational methodologies for real-space structural refinement of
large macromolecular complexes.
Boon Chong Goh, Jodi A. Hadden, Rafael C. Bernardi, Abhishek Singharoy, Ryan
McGreevy, Till Rudack, C. Keith Cassidy, and Klaus Schulten.
Annual Review of Biophysics, 45:253-278, 2016.
(PMC: PMC5526348) |
| 673. Advances in the molecular dynamics flexible fitting method for
cryo-EM modeling.
Ryan McGreevy, Ivan Teo, Abhishek Singharoy, and Klaus Schulten.
Methods, 100:50-60, 2016.
(PMC: PMC4848153) |
| 10133. Improving reaction kernel performance in Lattice Microbes:
particle-wise propensities and run-time generated code.
Michael J. Hallock and Zaida Luthey-Schulten.
pp. 428-434. IEEE, 2016.
|
| 672. Atomic detail visualization of photosynthetic membranes with
GPU-accelerated ray tracing.
John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek
Singharoy, Ivan Teo, Joao V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong
Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F.
Kourkoutis, C. Neil Hunter, and Klaus Schulten.
Parallel Computing, 55:17-27, 2016.
(PMC: PMC4890717) |
| 10126. Improved parameterization of amine-carboxylate and amine-phosphate
interactions for molecular dynamics simulations using the CHARMM and
AMBER force fields.
Jejoong Yoo and Aleksei Aksimentiev.
Journal of Chemical Theory and Computation, 12:430-443, 2016.
|
| 671. Intrinsic stepwise translocation of stretched ssDNA in graphene
nanopores.
Hu Qiu, Aditya Sarathy, Jean-Pierre Leburton, and Klaus Schulten.
Nano Letters, 15:8322-8330, 2015.
(PMC: PMC4676420) |
| 670. CryoEM and computer simulations reveal a novel kinase
conformational switch in bacterial chemotaxis signaling.
C. Keith Cassidy, Benjamin A. Himes, Frances J. Alvarez, Jun Ma, Gongpu Zhao,
Juan R. Perilla, Klaus Schulten, and Peijun Zhang.
eLife, 10.7554/eLife.08419, 2015.
PMID: 26583751.
|
| 669. Transient β-hairpin formation in α-synuclein monomer
revealed by coarse-grained molecular dynamics simulation.
Hang Yu, Wei Han, Wen Ma, and Klaus Schulten.
Journal of Chemical Physics, 143:243142, 2015.
(PMC: PMC4684271) |
| |
| 10123. Effects of dna replication on mrna noise.
Joseph R. Peterson, John A. Cole, Jingyi Fei, Taekjip Ha, and Zaida A.
Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
112:15886-15891, 2015.
(PMC: PMC4702981) |
| 668. Nascent peptide assists the ribosome in recognizing chemically
distinct small molecules.
Pulkit Gupta, Bo Liu, Dorota Klepacki, Vrinda Gupta, Klaus Schulten,
Alexander S. Mankin, and Nora Vazquez-Laslop.
Nature Chemical Biology, pp. (6 pages), 2015.
PMID: 26727240.
|
| 667. Dynamic allostery governs cyclophylin A-HIV capsid interplay.
Manman Lu, Guangjin Hou, Huilan Zhang, Christopher L. Suiter, Jinwoo Ahn,
In-Ja L. Byeon, Juan R. Perilla, Christopher J. Langmead, Ivan Hung, Peter L.
Gor'kov, Zhehong Gan, William Brey, Christopher Aiken, Peijun Zhang, Klaus
Schulten, Angela M. Gronenborn, and Tatyana Polenova.
Proceedings of the National Academy of Sciences, USA,
112:14617-14622, 2015.
(PMC: PMC4664340) |
| 10120. Molecular dynamics of membrane-spanning DNA channels: Conductance
mechanism, electro-osmotic transport and mechanical gating.
Jejoong Yoo and Aleksei Aksimentiev.
Journal of Physical Chemistry Letters, 6:4680-4687, 2015.
(NIHMS: PMID26551518) |
| 666. Chemical visualization of human pathogens: the Retroviral
Capsids.
Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten.
Proceedings of the 2015 ACM/IEEE Conference on
Supercomputing, 2015.
(4 pages).
|
| 665. Structural refinement of proteins by restrained molecular dynamics
simulations with non-interacting molecular fragments.
Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, and
Benoit Roux.
PLoS Computational Biology, 11:e1004368, 2015.
(19 pages).
(PMC: PMC4624691) |
| 664. Tri-Modal therapy: Combining hyperthermia with repurposed
bexarotene and ultrasound for treating liver cancer.
Santosh K. Misra, Goutam Ghoshal, Manas R. Gartia, Zhe Wu, Mao Ye, Corinne R.
Bromfield, Emery M. Williams, Krishnarao V. Tangella, Klaus Schulten,
Partha S. Ray, Everette C. Burdette, and Dipanjan Pan.
ACS Nano, 9:10695-10718, 2015.
(PMC: PMC4820022) |
| 10118. Atomic-level characterization of transport cycle thermodynamics in
the glycerol-3-phosphate:phosphate transporter.
Mahmoud Moradi, Giray Enkavi, and Emad Tajkhorshid.
Nature Communications, 6:8393, 2015.
(PMC: PMC4598623) |
| 10136. Towards a whole-cell model of ribosome biogenesis: Kinetic modeling
of SSU assembly.
Tyler M Earnest, Jonathan Lai, Ke Chen, Michael J Hallock, James R Williamson,
and Zaida Luthey-Schulten.
Biophysical Journal, 109:1117-1135, 2015.
(PMC: PMC4576174) |
| 10117. Incorporation of charged residues in the CYP2J2 FG loop disrupts
CYP2J2-lipid bilayer interactions.
Daniel R McDougle, Javier L Baylon, Daryl D Meling, Amogh Kambalyal, Yelena V
Grinkova, Jared Hammernik, Emad Tajkhorshid, and Aditi Das.
Biochimica et Biophysica Acta - Biomembranes, 1848:2460-2470,
2015.
(PMC: PMC4559526) |
| 663. Mapping mechanical force propagation through biomolecular complexes.
Constantin Schoeler, Rafael C. Bernardi, Klara H. Malinowska, Ellis Durner,
Wolfgang Ott, Edward A. Bayer, Klaus Schulten, Michael A. Nash, and
Hermann E. Gaub.
Nano Letters, 15:7370-7376, 2015.
(PMC: PMC4721519) |
| 662. Dynamic profiling of double-stranded RNA binding proteins.
Xinlei Wang, Lela Vukovic, Hye Ran Koh, Klaus Schulten, and Sua Myong.
Nucleic Acids Res., 43:7566-7576, 2015.
(PMC: PMC4551942) |
| 661. Macromolecular crystallography for synthetic abiological molecules:
Combining xMDFF and PHENIX for structure determination of cyanostar
macrocycles.
Abhishek Singharoy, Balasubramanian Venkatakrishnan, Yun Liu, Christopher G.
Mayne, Chun-Hsing Chen, Adam Zlotnick, Klaus Schulten, and Amar H. Flood.
Journal of the American Chemical Society, 137:8810-8818, 2015.
(PMC: PMC4504762) |
| 660. Atomic modeling of an immature retroviral lattice using molecular
dynamics and mutagenesis.
Boon Chong Goh, Juan R. Perilla, Matthew R. England, Katrina J. Heyrana,
Rebecca C. Craven, and Klaus Schulten.
Structure, 23:1414-1425, 2015.
(PMC: PMC4526393) |
| 10083. Runtime and architecture support for efficient data exchange in
multi-accelerator applications.
Javier Cabezas, Isaac Gelado, John E. Stone, Nacho Navarro, David B. Kirk, and
Wen-mei Hwu.
IEEE Transactions on Parallel and Distributed Systems,
26:1405-1418, May 2015.
(PMC: PMC4500157) |
| 658. Comparative dynamics and sequence dependence of DNA and RNA
binding to single walled carbon nanotubes.
Markita P. Landry, Lela Vukovic, Sebastian Kruss, Gili Bisker, Alexandra M.
Landry, Shahrin Islam, Rishabh Jain, Klaus Schulten, and Michael S. Strano.
Journal of Physical Chemistry C, 119:10048-10058, 2015.
(PMC: PMC4440682) |
| 10134. Computational characterization of structural dynamics underlying
function in active membrane transporters.
Jing Li, Po-Chao Wen, Mahmoud Moradi, and Emad Tajkhorshid.
Current Opinion in Structural Biology, 31:96-105, 2015.
(PMC: PMC4476910) |
| 10107. Redox potential tuning through differential quinone binding in the
photosynthetic reaction center of Rhodobacter sphaeroides.
Josh V. Vermaas, Alexander T. Taguchi, Sergel A. Dikanov, Colin A. Wraight, and
Emad Tajkhorshid.
Biochemistry, 54:2104-2116, 2015.
(NIHMS: 25734689) |
| 657. The ribosome can discriminate the chirality of amino acids within its
peptidyl-transferase center.
Michael T. Englander, Joshua L. Avins, Rachel C. Fleisher, Bo Liu, Philip R.
Effraim, Jiangning Wang, Klaus Schulten, Thomas S. Leyh, Ruben L. Gonzalez
Jr., and Virginia W. Cornish.
Proceedings of the National Academy of Sciences, USA,
112:6038-6043, 2015.
(PMC: PMC4434717) |
| 659. Comparing fast pressure jump and temperature jump protein folding
experiments and simulations.
Anna Jean Wirth, Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin
Gruebele.
Journal of the American Chemical Society, 137:7152-7159, 2015.
(PMC: PMC4794261) |
| 10135. Spatially-resolved metabolic cooperativity within dense bacterial
colonies.
John A Cole, Lars Kohler, Jamila Hedhli, and Zaida Luthey-Schulten.
BMC Systems Biology, 9:15, 2015.
(PMC: PMC4376365) |
| 10116. Mechanism of drug-drug interactions mediated by human cytochrome
P450 CYP3A4 monomer.
Ilia G. Denisov, Yelena V. Grinkova, Javier L. Baylon, Emad Tajkhorshid, and
Stephen G. Sligar.
Biochemistry, 54:2227-2239, 2015.
(PMC: PMC4757451) |
| 656. Molecular dynamics simulations of large macromolecular complexes.
Juan R. Perilla, Boon Chong Goh, C. Keith Cassidy, Bo Liu, Rafael C. Bernardi,
Till Rudack, Hang Yu, Zhe Wu, and Klaus Schulten.
Current Opinion in Structural Biology, 31:64-74, 2015.
(PMC: PMC4476923) |
| 655. Tunable graphene quantum point contact transistor for DNA detection
and characterization.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Nanotechnology, 26:134005, 2015.
(10 pages).
(PMC: PMC4400256) |
| 10121. Ionic conductivity, structural deformation, and programmable
anisotropy of DNA origami in electric field.
Chen-Yu Li, Elisa A. Hemmig, Jinglin Kong, Jejoong Yoo, Silvia
Hernández-Ainsa, Ulrich F. Keyser, and Aleksei Aksimentiev.
ACS Nano, 9:1420-1433, 2015.
PMID: 25623807.
(PMC: PMC4469488) |
| 654. Mechanism of substrate translocation by a ring-shaped ATPase motor
at millisecond resolution.
Wen Ma and Klaus Schulten.
Journal of the American Chemical Society, 137:3031-3040, 2015.
(PMC: PMC4393844) |
| 651. Identification of ubiquinol binding motifs at the Qo-site of the
cytochrome bc1 complex.
Angela M. Barragan, Antony R. Crofts, Klaus Schulten, and Ilia A. Solov'yov.
Journal of Physical Chemistry B, 119:433-447, 2015.
(PMC: PMC4297238) |
| 650. CheY's acetylation sites responsible for generating clockwise
flagellar rotation in Escherichia coli.
Milana Fraiberg, Oshri Afanzar, C. Keith Cassidy, Alexandra Gabashvili, Klaus
Schulten, Yishai Levin, and Michael Eisenbach.
Molecular Microbiology, 95:231-244, 2015.
(PMC: PMC4426874) |
| 649. Multiple-replica strategies for free-energy calculations in NAMD:
Multiple-walker adaptive biasing force and walker selection rules.
Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot.
Journal of Chemical Theory and Computation, 10:5276-5285,
2014.
|
| 647. Ultrastable cellulosome-adhesion complex tightens under load.
Constantin Schoeler, Klara H. Malinowska, Rafael C. Bernardi, Lukas F. Milles,
Markus A. Jobst, Ellis Durner, Wolfgang Ott, Daniel B. Fried, Edward A.
Bayer, Klaus Schulten, Hermann E. Gaub, and Michael A. Nash.
Nature Communications, 5:5635, 2014.
(PMC: PMC4266597) |
| 10103. Conformational heterogeneity of α-synuclein in membrane.
Josh V. Vermaas and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1838:3107-3117,
2014.
(PMC: PMC4194229) |
| 637. Gate-modulated graphene quantum point contact device for DNA
sensing.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Journal of Computational Electronics, 13:839-846, 2014.
(PMC: PMC4224323) |
| 646. Petascale Tcl with NAMD, VMD, and Swift/T.
James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong,
Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
In SC'14 workshop on High Performance Technical Computing in
Dynamic Languages, SC '14, pp. 6-17. IEEE Press, 2014.
|
| 645. Visualization of energy conversion processes in a light harvesting
organelle at atomic detail.
Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo,
Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C.
Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten.
In Proceedings of the International Conference on High
Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press,
2014.
(4 pages).
|
| 10084. Unlocking the full potential of the Cray XK7 accelerator.
Mark D. Klein and John E. Stone.
In Cray User Group Conference. Cray, May 2014.
|
| 640. Stable small quantum dots for synaptic receptor tracking on live
neurons.
En Cai, Pinghua Ge, Sang Hak Lee, Okunola Jeyifous, Yong Wang, Yanxin Liu,
Katie Wilson, Sung Jun Lim, Michelle Baird, John Stone, Kwan Young Lee,
Michael Davidson, Hee Jung Chung, Klaus Schulten, Andrew Smith, William
Green, and Paul R. Selvin.
Angewandte Chemie - International Edition in English,
126:12692-12696, 2014.
(PMC: PMC4240739) |
| 10105. Changing the peptide specificity of a human T-cell receptor by
directed evolution.
Sheena N. Smith, Yuhang Wang, Javier L. Baylon, Nishant K. Singh, Brian M.
Baker, Emad Tajkhorshid, and David M. Kranz.
Nature Communications, 5:5223, 2014.
(13 pages).
(PMC: PMC4225554) |
| 10104. Membrane-induced structural rearrangement and identification of a
novel membrane anchor in Talin F2F3.
Mark J. Arcario and Emad Tajkhorshid.
Biophysical Journal, 107:2059-2069, 2014.
(PMC: PMC4223205) |
| 643. A highly tilted membrane configuration for the pre-fusion state of
synaptobrevin.
Andrew E. Blanchard, Mark J. Arcario, Klaus Schulten, and Emad Tajkhorshid.
Biophysical Journal, 107:2112-2121, 2014.
(PMC: PMC4223215) |
| 10081. Methodologies for the analysis of instantaneous lipid diffusion in
MD simulations of large membrane systems.
Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E.
Stone, Bruno Jobard, and Mark S.P. Sansom.
Faraday Discussions, 169:455-475, 2014.
(PMC: PMC4208077) |
| 630. GPU-accelerated analysis and visualization of large structures
solved by molecular dynamics flexible fitting.
John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
Faraday Discussions, 169:265-283, 2014.
(PMC: PMC4208074) |
| 653. Enhanced sampling techniques in molecular dynamics simulations of
biological systems.
Rafael C. Bernardi, Marcelo C. R. Melo, and Klaus Schulten.
Biochimica et Biophysica Acta, 1850:872-877, 2015.
(PMC: PMC4339458) |
| 644. Electronic detection of dsDNA transition from helical to zipper
conformation using graphene nanopores.
Chaitanya Sathe, Anuj Girdhar, Jean-Pierre Leburton, and Klaus Schulten.
Nanotechnology, 25:445105, 2014.
(9 pages).
(PMC: PMC4244269) |
| 648. Die Geheimnisse des Lebens berechnen.
Till Rudack, Juan Perilla, and Klaus Schulten.
Spektrum der Wissenschaft, 11:86-95, November 2014.
|
| 652. Multilevel summation method for electrostatic force evaluation.
David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and
Klaus Schulten.
Journal of Chemical Theory and Computation, 11:766-779, 2015.
(PMC: PMC4325600) |
| 642. On the different types of vibrations interacting with electronic
excitations in the PE545 and FMO antenna systems.
Mortaza Aghtar, Johann Strümpfer, Carsten Olbrich, Klaus Schulten, and
Ulrich Kleinekathoefer.
Journal of Physical Chemistry Letters, 5:3131-3137, 2014.
|
| 641. Fibril elongation by Aβ17−42: Kinetic network analysis of
hybrid-resolution molecular dynamics simulations.
Wei Han and Klaus Schulten.
Journal of the American Chemical Society, 136:12450-12460,
2014.
(PMC: PMC4156860) |
| 639. Synaptotagmin's role in neurotransmitter release likely involves
Ca2+-induced conformational transition.
Zhe Wu and Klaus Schulten.
Biophysical Journal, 107:1156-1166, 2014.
(PMC: PMC4156666) |
| 619. Structure, function, and quantum dynamics of pigment-protein
complexes.
Ioan Kosztin and Klaus Schulten.
In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio,
editors, Quantum Effects in Biology, pp. 123-143. Cambridge University
Press, 2014.
|
| 621. Quantum biology of retinal.
Shigehiko Hayashi and Klaus Schulten.
In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio,
editors, Quantum Effects in Biology, pp. 237-263. Cambridge University
Press, 2014.
|
| 620. A chemical compass for bird navigation.
Ilia A. Solov'yov, P. J. Hore, Thorsten Ritz, and Klaus Schulten.
In Masoud Mohseni, Yasser Omar, Greg Engel, and Martin B. Plenio,
editors, Quantum Effects in Biology, chapter 10, pp. 218-236.
Cambridge University Press, 2014.
|
| 636. xMDFF: Molecular dynamics flexible fitting of low-resolution
X-Ray structures.
Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo
Perozo, and Klaus Schulten.
Acta Crystallographica D, 70:2344-2355, 2014.
(PMC: PMC4157446) |
| 10087. Mapping to irregular torus topologies and other techniques for
petascale biomolecular simulation.
James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V.
Kalé.
In Proceedings of the International Conference on High
Performance Computing, Networking, Storage and Analysis, SC '14, pp. 81-91.
IEEE Press, 2014.
(PMC: PMC4292797) |
| 638. A structural model of the active ribosome-bound membrane protein
insertase YidC.
Stephan Wickles, Abhishek Singharoy, Jessica Andreani, Stefan Seemayer, Lukas
Bischoff, Otto Berninghausen, Johannes Soeding, Klaus Schulten, Eli van der
Sluis, and Roland Beckmann.
eLife, 3:e03035, 2014.
(PMC: PMC4124156) |
| 633. Diffusive models of membrane permeation with explicit orientational
freedom.
Jeffrey Comer, Klaus Schulten, and Christophe Chipot.
Journal of Chemical Theory and Computation, 10:2710-2718,
2014.
|
| 635. Macrolide antibiotics allosterically predispose the ribosome for
translation arrest.
Shanmugapriya Sothiselvam, Bo Liu, Wei Han, Dorota Klepacki, Gemma C. Atkinson,
Age Brauer, Maido Remm, Tanel Tenson, Klaus Schulten, Nora
Vázquez-Laslop, and Alexander S. Mankin.
Proceedings of the National Academy of Sciences, USA,
111:9804-9809, 2014.
(PMC: PMC4103360) |
| 10085. Adaptive multilevel splitting in molecular dynamics simulations.
David Aristoff, Tony Lelièvre, Christopher G. Mayne, and Ivan Teo.
ESAIM: Proceedings and Surveys, 48:215-225, 2015.
(PMC: PMC4440697) |
| 10119. Computational recipe for efficient description of large-scale
conformational changes in biomolecular systems.
Mahmoud Moradi and Emad Tajkhorshid.
Journal of Chemical Theory and Computation, 10:2866-2880,
2014.
(PMC: PMC4089915) |
| 632. Substrate recognition and specificity of double-stranded RNA
binding proteins.
Lela Vukovic, Hye Ran Koh, Sua Myong, and Klaus Schulten.
Biochemistry, 53:3457-3466, 2014.
(PMC: PMC4051425) |
| 10130. A coarse-grained model of unstructured single-stranded DNA derived
from atomistic simulation and single-molecule experiment.
Christopher Maffeo, Thuy T. M. Ngo, Taekjip Ha, and Aleksei Aksimentiev.
Journal of Chemical Theory and Computation, 10:2891-2896,
2014.
(PMC: PMC4132850) |
| 631. Light harvesting by lamellar chromatophores in Rhodospirillum
photometricum.
Danielle Chandler, Johan Strümpfer, Melih Sener, Simon Scheuring, and Klaus
Schulten.
Biophysical Journal, 106:2503-2510, 2014.
(PMC: PMC4052275) |
| 634. Molecular dynamics study of enhanced Man5B enzymatic activity.
Rafael C. Bernardi, Isaac Cann, and Klaus Schulten.
Biotechnology for Biofuels, 7:1-8, 2014.
(PMC: PMC4074406) |
| 10106. Conformational dynamics of the nucleotide binding domains and the
power stroke of a heterodimeric ABC transporter.
Smriti Mishra, Brandy Verhalen, Richard A Stein, Po-Chao Wen, Emad Tajkhorshid,
and Hassane S Mchaourab.
eLife, 3:e02740, 2014.
(PMC: PMC4046567) |
| 10102. Conformational dynamics at the inner gate of KcsA during
activation.
Raymond E Hulse, Joseph R Sachleben, Po-Chao Wen, Mahmoud Moradi, Emad
Tajkhorshid, and Eduardo Perozo.
Biochemistry, 53:2557-2559, 2014.
(PMC: PMC4010282) |
| 10079. Partitioning of amino acids into a model membrane: Capturing the
interface.
Taras V. Pogorelov, Josh V. Vermaas, Mark J. Arcario, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 118:1481-1492, 2014.
|
| 10082. Simulation of reaction diffusion processes over biologically relevant
size and time scales using multi-GPU workstations.
Michael J. Hallock, John E. Stone, Elijah Roberts, Corey Fry, and Zaida
Luthey-Schulten.
Parallel Computing, 40:86-99, 2014.
(PMC: PMC4039640) |
| 629. CHARMM-GUI PACE CG builder for solution, micelle, and bilayer
coarse-grained simulations.
Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, and Wonpil Im.
Journal of Chemical Information and Modeling, 54:1003-1009,
2014.
|
| 623. Assembly of Nsp1 nucleoporins provides insight into nuclear pore
complex gating.
Ramya Gamini, Wei Han, John E. Stone, and Klaus Schulten.
PLoS Computational Biology, 10:e1003488, 2014.
(14 pages).
(PMC: PMC3952814) |
| 10124. Towards a computational model of a methane producing archaeum.
Joseph R Peterson, Piyush Labhsetwar, Jeremy R Ellermeier, Petra R A Kohler,
Ankur Jain, Taekjip Ha, William W Metcalf, and Zaida Luthey-Schulten.
Archaea, 2014, 2014.
(18 pages).
(PMC: PMC3960522) |
| 617. Generalized scalable multiple copy algorithms for molecular dynamics
simulations in NAMD.
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C.
Gumbart, Yun Luo, Klaus Schulten, and Benoît Roux.
Computer Physics Communications, 185:908-916, 2014.
(PMC: PMC4059768) |
| 10080. A microscopic view of phospholipid insertion into biological
membranes.
Josh V. Vermaas and Emad Tajkhorshid.
Journal of Physical Chemistry B, 118:1754-1764, 2014.
(PMC: PMC3933253) |
| 624. Single molecule FRET reveals pore size and opening mechanism of
MscL.
Yong Wang, Yanxin Liu, Hannah A. DeBerg, Takeshi Nomura, Melinda Tonks Hoffman,
Paul R. Rohde, Klaus Schulten, Boris Martinac, and Paul R. Selvin.
eLife, 3:e01834, 2014.
(21 pages).
|
| 627. Integration of energy and electron transfer processes in the
photosynthetic membrane of Rhodobacter sphaeroides.
Michaël L. Cartron, John D. Olsen, Melih Sener, Philip J. Jackson,
Amanda A. Brindley, Pu Qian, Mark J. Dickman, Graham J. Leggett, Klaus
Schulten, and C. Neil Hunter.
Biochimica et Biophysica Acta - Bioenergetics,
1837:1769-1780, 2014.
(PMC: PMC4143486) |
| 10086. Water access points and hydration pathways in CLC H+/Cl−
transporters.
Wei Han, Ricky C. Cheng, Merritt C. Maduke, and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
111:1819-1824, 2014.
(PMC: PMC3918786) |
| 622. Structural mechanism of voltage-dependent gating in an isolated
voltage-sensing domain.
Qufei Li, Sherry Wanderling, Marcin Paduch, David Medovoy, Abhishek Singharoy,
Ryan McGreevy, Carlos Villalba-Galea, Raymond E. Hulse, Benoit Roux, Klaus
Schulten, Anthony Kossiakoff, and Eduardo Perozo.
Nature Structural & Molecular Biology, 21:244-252, 2014.
(PMC: 4116111) |
| 618. Separation of photo-induced radical pair in cryptochrome to a
functionally critical distance.
Ilia Solov'yov, Tatiana Domratcheva, and Klaus Schulten.
Scientific Reports, 4:3845, 2014.
(8 pages).
(PMC: PMC4894384) |
| 625. Observation of complete pressure-jump protein refolding in molecular
dynamics simulation and experiment.
Yanxin Liu, Maxim B. Prigozhin, Klaus Schulten, and Martin Gruebele.
Journal of the American Chemical Society, 136:4265-4272, 2014.
|
| 626. Calculation of lipid-bilayer permeabilities using an average force.
Jeffrey Comer, Klaus Schulten, and Christophe Chipot.
Journal of Chemical Theory and Computation, 10:554-564, 2014.
|
| 10101. Mechanistic picture for conformational transition of a membrane
transporter at atomic resolution.
Mahmoud Moradi and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
110:18916-18921, 2013.
(PMC: PMC3839739) |
| 597. GPU-accelerated molecular visualization on petascale supercomputing
platforms.
John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
In Proceedings of the 8th International Workshop on Ultrascale
Visualization, UltraVis '13, pp. 6:1-6:8, New York, NY, USA, 2013. ACM.
|
| 598. Molecular mechanisms of inhibition of influenza by surfactant protein
D revealed by large-scale molecular dynamics simulation.
Boon Chong Goh, Michael J. Rynkiewicz, Tanya R. Cafarella, Mitchell R. White,
Kevan L. Hartshorn, Kimberly Allen, Erika C. Crouch, Oliviana Calin, Peter H.
Seeberger, Klaus Schulten, and Barbara A. Seaton.
Biochemistry, 52:8527-8538, 2013.
(PMC: PMC3927399) |
| 10122. In situ structure and dynamics of DNA origami determined through
molecular dynamics simulations.
Jejoong Yoo and Aleksei Aksimentiev.
Proceedings of the National Academy of Sciences, USA,
110:20099-20104, 2013.
(PMC: PMC3864285) |
| 628. Molecular insights into the membrane-associated phosphatidylinositol
4-kinase IIα.
Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun
Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun, and Chang Chen.
Nature Communications, 5:3552, 2014.
(PMC: PMC3974213) |
| 616. Graphene quantum point contact transistor for DNA sensing.
Anuj Girdhar, Chaitanya Sathe, Klaus Schulten, and Jean-Pierre Leburton.
Proceedings of the National Academy of Sciences, USA,
110:16748-16753, 2013.
(PMC: 3801026) |
| 615. A computational kinetic model of diffusion for molecular systems.
Ivan Teo and Klaus Schulten.
Journal of Chemical Physics, 139:121929, 2013.
(15 pages).
(PMC: 3795746) |
| 613. Rapid parameterization of small molecules using the Force Field
Toolkit.
Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, and James C.
Gumbart.
Journal of Computational Chemistry, 34:2757-2770, 2013.
(PMC: 3874408) |
| 10100. Characterizing a histidine switch controlling pH-dependent
conformational changes of the influenza virus hemagglutinin.
Mohamad R. Kalani, Abdulvahab Moradi, Mahmoud Moradi, and Emad Tajkhorshid.
Biophysical Journal, 105:993-1003, 2013.
(PMC: PMC3752100) |
| 596. Early experiences scaling VMD molecular visualization and analysis
jobs on Blue Waters.
John E. Stone, Barry Isralewitz, and Klaus Schulten.
In Extreme Scaling Workshop (XSW), 2013, pp. 43-50, Aug. 2013.
|
| 614. Characterization of folding mechanisms of Trp-cage and WW-domain
by network analysis of simulations with a hybrid-resolution model.
Wei Han and Klaus Schulten.
Journal of Physical Chemistry B, 117:13367-13377, 2013.
(PMC: 3811923) |
| 10137. Heterogeneity in protein expression induces metabolic variability in
a modeled Escherichia coli population.
Piyush Labhsetwar, John Andrew Cole, Elijah Roberts, Nathan D Price, and
Zaida A Luthey-Schulten.
Proceedings of the National Academy of Sciences, USA,
110:14006-14011, 2013.
(PMC: PMC3752265) |
| 10099. On the origin of large flexibility of P-glycoprotein in the
inward-facing state.
Po-Chao Wen, Brandy Verhalen, Stephan Wilkens, Hassane S. Mchaourab, and Emad
Tajkhorshid.
Journal of Biological Chemistry, 288:19211-19220, 2013.
(PMC: PMC3696692) |
| 10098. Movement of NH3 through the human urea transporter B: a new
gas channel.
R. Ryan Geyer, Raif Musa-Aziz, Giray Enkavi, Paween Mahinthichaichan, Emad
Tajkhorshid, and Walter F. Boron.
American Journal of Physiology - Renal Physiology,
304:F1447-F1457, 2013.
(PMC: PMC3680674) |
| 10097. Subangstrom resolution X-ray structure details aquaporin-water
interactions.
Urszula Kosinska Eriksson, Gerhard Fischer, Rosmarie Friemann, Giray Enkavi,
Emad Tajkhorshid, and Richard Neutze.
Science, 340:1346-1349, 2013.
(PMC: PMC4066176) |
| 610. Flexible interwoven termini determine the thermal stability of
thermosomes.
Kai Zhang, Li Wang, Yanxin Liu, Kwok-Yan Chan, Xiaoyun Pang, Klaus Schulten,
Zhiyang Dong, and Fei Sun.
Protein & Cell, 4:432-444, 2013.
(PMC: 3740188) |
| 10096. Characterizing the membrane-bound state of cytochrome P450 3A4:
Structure, depth of insertion, and orientation.
Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar, and Emad Tajkhorshid.
Journal of the American Chemical Society, 135:8542-8551, 2013.
(PMC: PMC3682445) |
| 612. Mature HIV-1 capsid structure by cryo-electron microscopy and
all-atom molecular dynamics.
Gongpu Zhao, Juan R. Perilla, Ernest L. Yufenyuy, Xin Meng, Bo Chen, Jiying
Ning, Jinwoo Ahn, Angela M. Gronenborn, Klaus Schulten, Christopher Aiken,
and Peijun Zhang.
Nature, 497:643-646, 2013.
(PMC: 3729984) |
| 611. The FMO complex in a glycerol-water mixture.
Mortaza Aghtar, Johan Strümpfer, Carsten Olbrich, Klaus Schulten, and
Ulrich Kleinekathoefer.
Journal of Physical Chemistry B, 117:7157-7163, 2013.
(PMC: 3714603) |
| 10095. Driven metadynamics: Reconstructing equilibrium free energies from
driven adaptive-bias simulations.
Mahmoud Moradi and Emad Tajkhorshid.
Journal of Physical Chemistry Letters, 4:1882-1887, 2013.
(PMC: PMC3688312) |
| 10094. Transient formation of water-conducting states in membrane
transporters.
Jing Li, Saher A. Shaikh, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad
Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
110:7696-7701, 2013.
(PMC: PMC3651479) |
| 608. Misplaced helix slows down ultrafast pressure-jump protein folding.
Maxim B. Prigozhin, Yanxin Liu, Anna Jean Wirth, Shobhna Kapoor, Roland Winter,
Klaus Schulten, and Martin Gruebele.
Proceedings of the National Academy of Sciences, USA,
110:8087-8092, 2013.
(PMC: 3657825) |
| 606. Detection and quantification of methylation in DNA using
solid-state nanopores.
Jiwook Shim, Gwendolyn I. Humphreys, Bala Murali Venkatesan, Jan Marie Munz,
Xueqing Zou, Chaitanya Sathe, Klaus Schulten, Farhad Kosari, Ann M. Nardulli,
George Vasmatzis, and Rashid Bashir.
Scientific Reports, 3:1389, 2013.
(8 pages).
(PMC: 3593219) |
| 10138. Dna looping increases the range of bistability in a stochastic model
of the lac genetic switch.
Tyler M Earnest, Elijah Roberts, Michael Assaf, Karin Dahmen, and Zaida
Luthey-Schulten.
Physical Biology, 10:026002, 2013.
|
| 607. Signaling mechanisms of LOV domains: new insights from molecular
dynamics studies.
Peter L. Freddolino, Kevin H. Gardner, and Klaus Schulten.
Photochemical & Photobiological Sciences, 12:1158-1170, 2013.
(PMC: 3679247) |
| 605. Mechanism of tetracycline resistance by ribosomal protection protein
Tet(O).
Wen Li, Gemma C. Atkinson, Nehal S. Thakor, Ülar Allas, Chuao-chao Lu,
Kwok-Yan Chan, Tanel Tenson, Klaus Schulten, Kevin S. Wilson, Vasili
Hauryliuk, and Joachim Frank.
4:1477, 2013.
(8 pages).
(PMC: 3576927) |
| 609. The mechanism of ubihydroquinone oxidation at the Qo-site of
the cytochrome bc1 complex.
Antony R. Crofts, Sangjin Hong, Charles Wilson, Rodney Burton, Doreen Victoria,
Chris Harrison, and Klaus Schulten.
Biochimica et Biophysica Acta, 1827:1362-1377, 2013.
(PMC: PMC3995752) |
| 10093. Visualizing functional motions of membrane transporters with
molecular dynamics simulations.
Saher A. Shaikh, Jing Li, Giray Enkavi, Po-Chao Wen, Zhijian Huang, and Emad
Tajkhorshid.
Biochemistry, 52:569-587, 2013.
(PMC: PMC3560430) |
| 10092. Simulation studies of the mechanism of membrane transporters.
Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang,
Saher A. Shaikh, and Emad Tajkhorshid.
In Luca Monticelli and Emppu Salonen, editors, Biomolecular
Simulations, volume 924 of Methods in Molecular Biology, pp. 361-405.
Humana Press, 2013.
|
| 10077. Optimizing fine-grained communication in a biomolecular simulation
application on Cray XK6.
Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V.
Kalé, and James C. Phillips.
In Proceedings of the 2012 ACM/IEEE conference on
Supercomputing, pp. 1-11, Salt Lake City, Utah, 2012. IEEE press.
|
| |
| 604. Reconciling the roles of kinetic and thermodynamic factors in
membrane-protein insertion.
James C. Gumbart, Ivan Teo, Benoit Roux, and Klaus Schulten.
Journal of the American Chemical Society, 135:2291-2297, 2013.
(PMC: 3573731) |
| 572. Further optimization of a hybrid united-atom and coarse-grained force
field for folding simulations: Improved backbone hydration and interactions
between charged side chains.
Wei Han and Klaus Schulten.
Journal of Chemical Theory and Computation, 8:4413-4424, 2012.
(PMC: 3507460) |
| 10078. Lattice microbes: High-performance stochastic simulation method for
the reaction-diffusion master equation.
Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
Journal of Computational Chemistry, 34:245-255, 2013.
|
| 594. Molecular basis of drug resistance in A/H1N1 virus.
Ariela Vergara-Jaque, Horacio Poblete, Eric Lee, Klaus Schulten, Fernando
González-Nilo, and Christophe Chipot.
Journal of Chemical Information and Modeling, 52:2650-2656,
2012.
(PMC: DNA/NIH) |
| 602. DNA target sequence identification mechanism for dimer-active
protein complexes.
Markita P. Landry, Xueqing Zou, Lei Wang, Wai Mun Huang, Klaus Schulten, and
Yann R. Chemla.
Nucleic Acids Research, 41:2416-2427, 2013.
(PMC: 3575837) |
| 589. Identification of an N-terminal inhibitory extension as the primary
mechanosensory regulator of twitchin kinase.
Eleonore von Castelmur, Johan Strümpfer, Barbara Franke, Julijus
Bogomolovas, Sonia Barbieri, Hiroshi Qadota, Petr V. Konarev, Dmitri I.
Svergun, Siegfried Labeit, Guy M. Benian, Klaus Schulten, and Olga Mayans.
Proceedings of the National Academy of Sciences, USA,
109:13608-13613, 2012.
(PMC: 3427058) |
| 601. Membrane sculpting by F-BAR domains studied by molecular dynamics
simulations.
Hang Yu and Klaus Schulten.
PLoS Computational Biology, 9:e1002892, 2013.
(PMC: 3561051) |
| 590. Excited state dynamics in photosynthetic reaction center and light
harvesting complex 1.
Johan Strümpfer and Klaus Schulten.
Journal of Chemical Physics, 137:065101, 2012.
(8 pages).
(PMC: 3427344) |
| 600. Atomic model of rabbit hemorrhagic disease virus by cryo-electron
microscopy and crystallography.
Xue Wang, Fengting Xu, Jiasen Liu, Bingquan Gao, Yanxin Liu, Yujia Zhai, Jun
Ma, Kai Zhang, Timothy S. Baker, Klaus Schulten, Dong Zheng, Hai Pang, and
Fei Sun.
PLoS Pathogens, 9:e1003132, 2013.
(14 pages).
(PMC: 3547835) |
| 10091. Structure and permeation mechanism of a mammalian urea transporter.
Elena J Levin, Yu Cao, Giray Enkavi, Matthias Quick, Yaping Pan, Emad
Tajkhorshid, and Ming Zhou.
Proceedings of the National Academy of Sciences, USA,
109:11194-11199, 2012.
(PMC: PMC3396522) |
| 599. Effects of cytosine hydroxymethylation on DNA strand separation.
Philip M.D. Severin, Xueqing Zou, Klaus Schulten, and Hermann E. Gaub.
Biophysical Journal, 104:208-215, 2013.
(PMC: 3540242) |
| 595. Decrypting cryptochrome: Revealing the molecular identity of the
photoactivation reaction.
Ilia A. Solov'yov, Tatiana Domratcheva, Abdul R. M. Shahi, and Klaus Schulten.
Journal of the American Chemical Society, 134:18046-18052,
2012.
(PMC: 3500783) |
| 587. Open quantum dynamics calculations with the hierarchy equations of
motion on parallel computers.
Johan Strümpfer and Klaus Schulten.
Journal of Chemical Theory and Computation, 8:2808-2816, 2012.
(PMC: 3480185) |
| 583. Juxtaposing density matrix and classical path-based wave packet
dynamics.
Mortaza Aghtar, Jörg Liebers, Johan Strümpfer, Klaus Schulten, and
Ulrich Kleinekathöfer.
Journal of Chemical Physics, 136:214101, 2012.
(9 pages).
(PMC: PMC3376871) |
| 10090. Tissue factor/factor VIIa complex: Role of the membrane surface.
James H. Morrissey, Emad Tajkhorshid, Stephen G. Sligar, and Chad M. Rienstra.
Thrombosis Research, 129:S8-S10, 2012.
(PMC: PMC3335922) |
| 10075. Functional interplay between acetylation and methylation of the
RelA subunit of NF-κB.
X.-D. Yang, E. Tajkhorshid, and L.-F. Chen.
Molecular and Cellular Biology, 30:2170-2180, 2010.
|
| 10076. Control of nanoscale environment to improve stability of immobilized
proteins on diamond surfaces.
Adarsh D. Radadia, Courtney J. Stavis, Rogan Carr, Hongjun Zeng, William P.
King, John A. Carlisle, Aleksei Aksimentiev, Robert J. Hamers, and Rashid
Bashir.
Advanced Functional Materials, 21:1040-1050, 2011.
|
| 10071. Slowing the translocation of double-stranded DNA using a nanopore
smaller than the double helix.
U. Mirsaidov, J. Comer, V. Dimitrov, A. Aksimentiev, and G. Timp.
Nanotechnology, 21:395501-10, 2010.
|
| 10074. The binding interface of cytochrome c and cytochrome c1 in the
bc1 complex: rationalizing the role of key residues.
O. Kokhan, C. Wraight, and E. Tajkhorshid.
Biophysical Journal, 99:2647-2656, 2010.
|
| 10072. Surface functionalization of thin-film diamond for highly stable and
selective biological interfaces.
C. Stavis, T. L. Clare, J. E. Butler, A. D. Radadia, R. Carr, H. Zeng, W. King,
J. A. Carlisle, A. Aksimentiev, R. Bashir, and R.J. Hamers.
Proceedings of the National Academy of Sciences, USA,
108:983-988, 2011.
|
| 10073. The effect of calcium on the conformation of cobalamin transporter
BtuB.
B. Luan, M. Caffrey, and A. Aksimentiev.
PROTEINS: Structure, Function, and Bioinformatics,
78:1153-1162, 2010.
|
| 10070. Accelerating membrane insertion of peripheral proteins with a novel
membrane mimetic model.
Y. Zenmei Ohkubo, Taras V. Pogorelov, Mark J. Arcario, Geoff A. Christensen,
and Emad Tajkhorshid.
Biophysical Journal, 102:2130-2139, 2012.
|
| 603. Fusion pore formation and expansion induced by Ca2+ and
synaptotagmin 1.
Ying Lai, Jiajie Diao, Yanxin Liu, Yuji Ishitsuka, Zengliu Su, Klaus Schulten,
Taekjip Ha, and Yeon-Kyun Shin.
Proceedings of the National Academy of Sciences, USA,
110:1333-1338, 2013.
(PMC: 3557091) |
| 591. Vibrationally assisted electron transfer mechanism of olfaction: Myth
or reality?
Ilia A. Solov'yov, Po-Yao Chang, and Klaus Schulten.
Physical Chemistry - Chemical Physics, 14:13861-13871, 2012.
(PMC: 3478898) |
| 588. GPU/CPU algorithm for generalized Born / solvent-accessible
surface area implicit solvent calculations.
David E. Tanner, James C. Phillips, and Klaus Schulten.
Journal of Chemical Theory and Computation, 8:2521-2530, 2012.
(PMC: 3464051) |
| 582. Mutation of conserved histidines alters the tertiary structure and
nanomechanics of consensus ankyrin repeats.
Whasil Lee, Johan Strümpfer, Vann Bennett, Klaus Schulten, and Piotr E.
Marszalek.
Journal of Biological Chemistry, 287:19115-19121, 2012.
(PMC: 3365944) |
| 593. Electrically induced conformational change of peptides on metallic
nano-surfaces.
Yi Chen, Eduardo R. Cruz-Chu, Jaie Woodard, Manas Ranjan Gartia, Klaus
Schulten, and Logan Liu.
ACS Nano, 6:8847-8856, 2012.
(PMC: 3482133) |
| 585. Mechanisms of SecM-mediated stalling in the ribosome.
James Gumbart, Eduard Schreiner, Daniel N. Wilson, Roland Beckmann, and Klaus
Schulten.
Biophysical Journal, 103:331-341, 2012.
(PMC: 3400775) |
| 10089. Structural basis for iron piracy by pathogenic neisseria.
Nicholas Noinaj, Nicole C. Easley, Muse Oke, Naoko Mizuno, James Gumbart, Evzen
Boura, Ashley N. Steere, Olga Zak, Philip Aisen, Emad Tajkhorshid, Robert W.
Evans, Andrew R. Gorringe, Anne B. Mason, Alasdair C. Steven, and Susan K.
Buchanan.
Nature, 483:53-58, 2012.
(PMC: PMC3292680) |
| 586. Unique sugar-binding site mediates the distinct anti-influenza
activity of pig surfactant protein D.
Martin van Eijk, Michael J. Rynkiewicz, Mitchell R. White, Kevan L. Hartshorn,
Xueqing Zou, Klaus Schulten, Dong Luo, Erika C. Crouch, Tanya M. Cafarella,
James F. Head, Henk P. Haagsman, and Barbara A. Seaton.
Journal of Biological Chemistry, 287:26666-26677, 2012.
(PMC: 3411006) |
| 576. How quantum coherence assists photosynthetic light harvesting.
Johan Strumpfer, Melih Sener, and Klaus Schulten.
Journal of Physical Chemistry Letters, 3:536-542, 2012.
(PMC: 3404497) |
| 10068. Nanopore analysis of individual RNA/antibiotic complexes.
S. Wanunu, S. Bhattacharya, Y. Xie, Y. Tor, A. Aksimentiev, and M. Drndic.
ACS Nano, 5:9345-9353, 2011.
|
| 10066. ATP hydrolysis at one of the two sites in ABC transporters
initiates transport related conformational transitions.
G. Gyimesi, S. Ramachandran, P. Kota, N. V. Dokholyan, B. Sarkadi, and
T. Hegedus.
Biochimica et Biophysica Acta, 1808:2954-2964, 2011.
|
| 10069. Nucleotide discrimination with DNA immobilized in the MspA
nanopore.
E. A. Manrao, I. M. Derrington, M. Pavlenok, M. Niederweis, and J. H. Gundlach.
PLoS One, 6(10):e25723, 2011.
|
| 10067. Predicting the DNA sequence dependence of nanopore ion current
using atomic-resolution Brownian dynamics.
J. Comer and A. Aksimentiev.
Journal of Physical Chemistry C, 116:3376-3393, 2012.
|
| 10065. A gate-free pathway for substrate release from the inward-facing
state of the Na+-galactose transporter.
Jing Li and Emad Tajkhorshid.
Biochimica et Biophysica Acta - Biomembranes, 1818:263-271,
2012.
|
| 10132. End-to-end attraction of duplex DNA.
Christopher Maffeo, Binquan Luan, and Aleksei Aksimentiev.
Nucleic Acids Research, 40:3812-3821, 2012.
(PMC: PMC3351176) |
| 581. Structural characterization of λ-repressor folding from
all-atom molecular dynamics simulations.
Yanxin Liu, Johan Strümpfer, Peter L. Freddolino, Martin Gruebele, and
Klaus Schulten.
Journal of Physical Chemistry Letters, 3:1117-1123, 2012.
(PMC: 3377354) |
| 10088. Molecular basis for the activation of a catalytic asparagine residue
in a self-cleaving bacterial autotransporter.
Travis J. Barnard, James Gumbart, Janine H. Peterson, Nicholas Noinaj,
Nicole C. Easley, Nathalie Dautin, Adam J. Kuszak, Emad Tajkhorshid,
Harris D. Bernstein, and Susan K. Buchanan.
Journal of Molecular Biology, 415:128-142, 2012.
(PMC: PMC3230255) |
| 580. Fast visualization of Gaussian density surfaces for molecular
dynamics and particle system trajectories.
Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten.
In EuroVis - Short Papers 2012, pp. 67-71, 2012.
|
| 584. Quantum and classical dynamics simulations of ATP hydrolysis in
solution.
Christopher Harrison and Klaus Schulten.
Journal of Chemical Theory and Computation, 8:2328-2335, 2012.
(PMC: 3536536) |
| 10131. Improved parametrization of Li+, Na+,
K+, and Mg2+.
J. Yoo and A. Aksimentiev.
Journal of Physical Chemistry Letters, 3:45-50, 2012.
|
| 578. Structural characterization of mRNA-tRNA translocation
intermediates.
Xabier Agirrezabala, Hstau Liao, Eduard Schreiner, Jie Fu, Rodrigo Ortiz-Meoz,
Klaus Schulten, Rachel Green, and Joachim Frank.
Proceedings of the National Academy of Sciences, USA,
109:6094-6099, 2012.
(PMC: 3340995) |
| 579. Cryo-electron microscopy modeling by the molecular dynamics flexible
fitting method.
Kwok-Yan Chan, Leonardo G. Trabuco, Eduard Schreiner, and Klaus Schulten.
Biopolymers, 97:678-686, 2012.
(PMC: 3376020) |
| 10063. Capturing spontaneous partitioning of peripheral proteins using a
biphasic membrane-mimetic model.
Mark J. Arcario, Y. Zenmei Ohkubo, and Emad Tajkhorshid.
Journal of Physical Chemistry B, 115:7029-7037, 2011.
|
| 10064. Membrane transporters: Molecular machines coupling cellular energy to
vectorial transport across the membrane.
Zhijian Huang, Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Jing Li, and Emad
Tajkhorshid.
In Benoit Roux, editor, Molecular Machines, chapter 9, pp.
151-182. World Scientific Publishing, Singapore, 2011.
|
| 557. Parallel generalized Born implicit solvent calculations with
NAMD.
David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten.
Journal of Chemical Theory and Computation, 7:3635-3642, 2011.
(PMC: 3222955) |
| 574. Recognition of methylated DNA through methyl-CpG binding domain
proteins.
Xueqing Zou, Wen Ma, Ilia Solov'yov, Christophe Chipot, and Klaus Schulten.
Nucleic Acids Research, 40:2747-2758, 2012.
(PMC: 3315304) |
| 558. Computational investigation of DNA detection using graphene
nanopores.
Chaitanya Sathe, Xueqing Zou, Jean-Pierre Leburton, and Klaus Schulten.
ACS Nano, 5:8842-8851, 2011.
(PMC: 3222720) |
| 10062. Nanoscale studies of protein-membrane interactions in blood clotting.
James H. Morrissey, Emad Tajkhorshid, and Chad M. Rienstra.
Journal of Thrombosis and Haemostasis, 9 (Suppl. 1):167-167,
2011.
(PMC: PMC3151027) |
| 10061. Atomic view of calcium-induced clustering of phosphatidylserine in
mixed lipid bilayers.
John M. Boettcher, Rebecca L. Davis-Harrison, Mary C. Clay, Andrew J.
Nieuwkoop, Y. Zenmei Ohkubo, Emad Tajkhorshid, James H. Morrissey, and
Chad M. Rienstra.
Biochemistry, 50:2264-2273, 2011.
(PMC: 3069658) |
| 10060. Molecular determinants of phospholipid synergy in blood clotting.
Narjes Tavoosi, Rebecca L. Davis-Harrison, Taras V. Pogorelov, Y. Zenmei
Ohkubo, Mark J. Arcario, Mary C. Clay, Chad M. Rienstra, Emad Tajkhorshid,
and James H. Morrissey.
Journal of Biological Chemistry, 286:23247-23253, 2011.
(PMC: 3123091) |
| 10059. Enabling and scaling biomolecular simulations of 100 million atoms on
petascale machines with a multicore-optimized message-driven runtime.
Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kalé,
James C. Phillips, and Chris Harrison.
In Proceedings of the 2011 ACM/IEEE conference on
Supercomputing, pp. 61:1-61:11, Seattle, WA, November 2011.
|
| 10140. Microscopic perspective on the adsorption isotherm of a heterogeneous
surface.
Rogan Carr, Jeffrey Comer, Mark D. Ginsberg, and Aleksei Aksimentiev.
Journal of Physical Chemistry Letters, 2:1804-1807, 2011.
(PMC: PMC3353733) |
| 575. Molecular dynamics investigation of the ω current in the
Kv1.2 voltage sensor domains.
Fatemeh Khalili-Araghi, Emad Tajkhorshid, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 102:258-267, 2012.
(PMC: 3260662) |
| 569. Theory and simulation of the environmental effects on FMO
electronic transitions.
Carsten Olbrich, Johan Strümpfer, Klaus Schulten, and Ulrich
Kleinekathoefer.
Journal of Physical Chemistry Letters, 2:1771-1776, 2011.
(PMC: 3144632) |
| 571. Symmetry-restrained flexible fitting for symmetric EM maps.
Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor
Sewell, and Klaus Schulten.
Structure, 19:1211-1218, 2011.
(PMC: 3412758) |
| 568. Immersive out-of-core visualization of large-size and long-timescale
molecular dynamics trajectories.
John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
Lecture Notes in Computer Science, 6939:1-12, 2011.
(PMC: 3032211) |
| 570. Oligomerization state of photosynthetic core complexes is correlated
with the dimerization affinity of a transmembrane helix.
Jen Hsin, Loren LaPointe, Alla Kazy, Christophe Chipot, Alessandro Senes, and
Klaus Schulten.
Journal of the American Chemical Society, 133:14071-14081,
2011.
(PMC: 3168531) |
| 10049. Structural basis of substrate selectivity in the
glycerol-3-phosphate:phosphate antiporter GlpT.
Christopher J. Law, Giray Enkavi, Da-Neng Wang, and Emad Tajkhorshid.
Biophysical Journal, 97:1346-1353, 2009.
|
| 10054. GPU clusters for high performance computing.
Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen
Arnold, John E. Stone, James Phillips, and Wen-mei Hwu.
In Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE
International Conference on, pp. 1-8, 2009.
|
| 10056. An asymmetric distributed shared memory model for heterogeneous
parallel system.
Isaac Gelado, John E. Stone, Javier Cabezas, Sanjay Patel, Nacho Navarro, and
Wen-mei W. Hwu.
In ASPLOS '10: Proceedings of the 15th International Conference
on Architectural Support for Programming Languages and Operating Systems,
pp. 347-358, 2010.
|
| 10053. Visualization of cyclic and multi-branched molecules with VMD.
Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
Journal of Molecular Graphics and Modelling, 28:131-139, 2009.
(NIHMS: 215013) |
| 10055. Probing biomolecular machines with graphics processors.
James C. Phillips and John E. Stone.
Communications of the ACM, 52:34-41, 2009.
|
| 10057. Quantifying the impact of GPUs on performance and energy efficiency
in HPC clusters.
Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman, Guochun Shi,
Kenneth Esler, Volodymyr Kindratenko, John E. Stone, and James C. Phillips.
In International Conference on Green Computing, pp. 317-324,
2010.
|
| 566. From atomistic modeling to excitation transfer and two-dimensional
spectra of the FMO light-harvesting complex.
Carsten Olbrich, Thomas L. C. Jansen, Jörg Liebers, Mortaza Aghtar, Johan
Strümpfer, Klaus Schulten, Jasper Knoester, and Ulrich Kleinekathoefer.
Journal of Physical Chemistry B, 115(26):8609-8621, 2011.
(PMC: 3140161) |
| 10139. Noise contributions in an inducible genetic switch: a whole-cell
simulation study.
Elijah Roberts, Andrew Magis, Julio O Ortiz, Wolfgang Baumeister, and Zaida
Luthey-Schulten.
PLoS Computational Biology, 7:e1002010, 2011.
(PMC: PMC3053318) |
| 561. Free energy of nascent-chain folding in the translocon.
James Gumbart, Christophe Chipot, and Klaus Schulten.
Journal of the American Chemical Society, 133:7602-7607, 2011.
(PMC: 3100187) |
| 592. The p7 protein of hepatitis C virus forms structurally plastic,
minimalist ion channels.
Danielle E. Chandler, Francois Penin, Klaus Schulten, and Christophe Chipot.
PLoS Computational Biology, 8:e1002702, 2012.
(10 pages).
(PMC: 3447957) |
| 10058. Fast analysis of molecular dynamics trajectories with graphics
processing units-radial distribution function histogramming.
Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer.
Journal of Computational Physics, 230:3556-3569, 2011.
(PMC: PMC3085256) |
| 560. Domain motion of individual F1-ATPase β-subunits during
unbiased molecular dynamics simulations.
Ulrich Kleinekathoefer, Barry Isralewitz, Markus Dittrich, and Klaus Schulten.
Journal of Physical Chemistry, 115:7267-7274, 2011.
(PMC: 3121902) |
| 552. 3rd generation DNA sequencing with a nanopore.
Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang,
Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony Ho,
Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten.
In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing
and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer,
Berlin, 2011.
|
| 564. Stereochemical errors and their implications for molecular dynamics
simulations.
Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, and Klaus Schulten.
BMC Bioinformatics, 12:190, 2011.
(9 pages).
(PMC: 3124434) |
| 577. Reaction kinetics and mechanism of magnetic field effects in
cryptochrome.
Ilia A. Solov'yov and Klaus Schulten.
Journal of Physical Chemistry B, 116:1089-1099, 2012.
(PMC: 3266978) |
| 567. Cytosine methylation alters DNA mechanical properties.
Philip M.D. Severin, Xueqing Zou, Hermann E. Gaub, and Klaus Schulten.
Nucleic Acids Research, 39:8740-8751, 2011.
(PMC: 3203585) |
| 554. Structural insights into cognate vs. near-cognate discrimination
during decoding.
Xabier Agirrezabala, Eduard Schreiner, Leonardo G. Trabuco, Jianlin Lei,
Rodrigo F. Ortiz-Meoz, Klaus Schulten, Rachel Green, and Joachim Frank.
EMBO Journal, 30:1497-1507, 2011.
(PMC: 3102289) |
| 563. Extension of a three-helix bundle domain of myosin VI and key role
of calmodulins.
Yanxin Liu, Jen Hsin, HyeongJun Kim, Paul R Selvin, and Klaus Schulten.
Biophysical Journal, 100:2964-2973, 2011.
(PMC: 3123929) |
| 546. Molecular dynamics of EF-G during translocation.
Wen Li, Leonardo G. Trabuco, Klaus Schulten, and Joachim Frank.
PROTEINS: Structure, Function, and Bioinformatics,
79:1478-1486, 2011.
(PMC: 3132869) |
| 551. Improved resolution of tertiary structure elasticity in muscle
protein.
Jen Hsin and Klaus Schulten.
Biophysical Journal, 100:L22-L24, 2011.
(PMC: 3037604) |
| 542. Quest for spatially correlated fluctuations in the FMO
light-harvesting complex.
Carsten Olbrich, Johan Strümpfer, Klaus Schulten, and Ulrich
Kleinekathoefer.
Journal of Physical Chemistry B, 115:758-764, 2011.
(PMC: 3244696) |
| 549. Förster energy transfer theory as reflected in the structures of
photosynthetic light harvesting systems.
Melih Sener, Johan Strümpfer, Jen Hsin, Danielle Chandler, Simon Scheuring,
C. Neil Hunter, and Klaus Schulten.
ChemPhysChem, 12:518-531, 2011.
(PMC: 3098534) |
| 556. The effect of correlated bath fluctuations on exciton transfer.
Johan Strümpfer and Klaus Schulten.
Journal of Chemical Physics, 134:095102, 2011.
(9 pages).
(PMC: 3064689) |
| 547. High-performance scalable molecular dynamics simulations of a
polarizable force field based on classical Drude oscillators in NAMD.
Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell Jr., Klaus
Schulten, and Benoît Roux.
Journal of Physical Chemistry Letters, 2:87-92, 2011.
(PMC: 3092300) |
| 559. Modulating LOV domain photodynamics with a residue alteration
outside the chromophore binding site.
Sang-Hun Song, Peter Freddolino, Abigail Nash, Elizabeth Carroll, Klaus
Schulten, Kevin Gardner, and Delmar S. Larsen.
Biochemistry, 50:2411-2423, 2011.
(PMC: 3068209) |
| 10129. DNA-DNA interactions in tight supercoils are described by a small
effective charge density.
Christopher Maffeo, Robert Schöpflin, Hergen Brutzer, René Stehr,
Aleksei Aksimentiev, Gero Wedemann, and Ralf Seidel.
Physical Review Letters, 105:158101, 2010.
(PMC: PMC3170404) |
| 10052. Modeling and dynamics of the inward-facing state of a
Na+/Cl− dependent neurotransmitter transporter homologue.
Saher Afshan Shaikh and Emad Tajkhorshid.
PLoS Computational Biology, 6:e1000905, 2010.
(PMC: PMC2928745) |
| 550. Free-energy cost for translocon-assisted insertion of membrane
proteins.
James Gumbart, Christophe Chipot, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
108:3596-3601, 2011.
(PMC: PMC3048118) |
| 562. Theoretical and computational investigation of flagellin
translocation and bacterial flagellum growth.
David E. Tanner, Wen Ma, Zhongzhou Chen, and Klaus Schulten.
Biophysical Journal, 100:2548-2556, 2011.
(PMC: 3117181) |
| 544. The light-harvesting apparatus in purple photosynthetic bacteria,
introduction to a quantum biological device.
Johan Strümpfer, Jen Hsin, Melih Sener, Danielle Chandler, and Klaus
Schulten.
In Benoit Roux, editor, Molecular Machines, chapter 2, pp.
19-48. World Scientific Press, 2011.
|
| 543. Viewing the mechanisms of translation through the computational
microscope.
James Gumbart, Eduard Schreiner, Leonardo G. Trabuco, Kwok-Yan Chan, and Klaus
Schulten.
In Joachim Frank, editor, Molecular Machines in Biology,
chapter 8, pp. 142-157. Cambridge University Press, 2011.
|
| 537. Immersive molecular visualization and interactive modeling with
commodity hardware.
John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten.
Lecture Notes in Computer Science, 6454:382-393, 2010.
|
| 545. Molecular origin of the hierarchical elasticity of titin: simulation,
experiment and theory.
Jen Hsin, Johan Strümpfer, Eric H. Lee, and Klaus Schulten.
Annual Review of Biophysics, 40:187-203, 2011.
|
| 534. Lipid-protein correlations in nanoscale phospholipid bilayers
determined by solid-state nuclear magnetic resonance.
Aleksandra Kijac, Amy Y. Shih, Andrew J. Nieuwkoop, Klaus Schulten, Stephen G.
Sligar, and Chad Rienstra.
Biochemistry, 49:9190-9198, 2010.
(PMC: PMC3136391) |
| 10036. Molecular mechanisms of active transport across the cellular
membrane, chapter 10, pp. 248-286.
Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad
Tajkhorshid.
Royal Society of Chemistry, 2010.
|
| 548. Molecular dynamics simulations of forced unbending of integrin
αVβ3.
Wei Chen, Jizhong Lou, Jen Hsin, Klaus Schulten, Stephen C. Harvey, and Cheng
Zhu.
PLoS Computational Biology, 7(2):e1001086, 2011.
(13 pages).
(PMC: 3040657) |
| 10141. Mechanical properties of a complete microtubule revealed through
molecular dynamics simulation.
David B. Wells and Aleksei Aksimentiev.
Biophysical Journal, 99:629-637, 2010.
(PMC: PMC2905083) |
| 10051. Protein membrane interactions: blood clotting on nanoscale bilayer.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, C. M. Rienstra,
A. Z. Kijac, Y. Z. Ohkubo, and E. Tajkhorshid.
Journal of Thrombosis and Haemostasis, 7:169-172, 2009.
|
| 10050. Tyrosine phosphorylation by Src within the cavity of the adenine
nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria.
Jianhua Feng, Eliana Lucchinetti, Giray Enkavi, Yi Wang, Peter Gehrig, Bernd
Roschitzki, Marcus C. Schaub, Emad Tajkhorshid, Kathrin Zaugg, and Michael
Zaugg.
American Journal of Physiology, 298:C740-748, 2010.
(PMC: 2838572) |
| 10048. Identification of the third Na+ site and the sequence of
extracellular binding events in the glutamate transporter.
Zhijian Huang and Emad Tajkhorshid.
Biophysical Journal, 99:1416-1425, 2010.
(PMC: PMC2931724) |
| 535. Formation of salt bridges mediates internal dimerization of myosin
VI medial tail domain.
HyeongJun Kim, Jen Hsin, Yanxin Liu, Paul R. Selvin, and Klaus Schulten.
Structure, 18:1443-1449, 2010.
(PMC: 3027149) |
| 541. Applications of the molecular dynamics flexible fitting method.
Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth
Villa, and Klaus Schulten.
Journal of Structural Biology, 173:420-427, 2011.
(PMC: 3032011) |
| 536. The role of L1 stalk-tRNA interaction in the ribosome elongation
cycle.
Leonardo G. Trabuco, Eduard Schreiner, John Eargle, Peter Cornish, Taekjip Ha,
Zaida Luthey-Schulten, and Klaus Schulten.
Journal of Molecular Biology, 402:741-760, 2010.
(PMC: 2967302) |
| 10047. OpenCL: A parallel programming standard for heterogeneous computing
systems.
John E. Stone, David Gohara, and Guochun Shi.
Computing in Science and Engineering, 12:66-73, 2010.
(PMC: 2964860) |
| 538. GPU algorithms for molecular modeling.
John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten.
In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors,
Scientific Computing with Multicore and Accelerators, chapter 16, pp.
351-371. Chapman & Hall/CRC Press, 2011.
|
| 525. How birds and other animals orient in the Earth magnetic field.
Ilia A. Solov'yov, Klaus Schulten, and Walter Greiner.
Physik Journal, 9:23-28, 2010.
(article in German only).
(NIHMS: 280922) |
| 528. Flow-induced β-hairpin folding of the glycoprotein Ibα
β-switch.
Xueqing Zou, Yanxin Liu, Zhongzhou Chen, Gloria Ines Cárdenas-Jirón,
and Klaus Schulten.
Biophysical Journal, 99:1182-1191, 2010.
(PMC: 2920744) |
| 10043. Nitric oxide conduction by the brain aquaporin AQP4.
Yi Wang and Emad Tajkhorshid.
PROTEINS: Structure, Function, and Bioinformatics, 78:661-670,
2010.
|
| 10044. Ion-releasing state of a secondary membrane transporter.
Jing Li and Emad Tajkhorshid.
Biophysical Journal, 97:L29-L31, 2009.
|
| 10046. Capturing functional motions of membrane channels and transporters
with molecular dynamics simulation.
Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Zhijian Huang, and Emad
Tajkhorshid.
Journal of Computational and Theoretical Nanosciences,
7:2481-2500, 2010.
|
| 10042. Dynamical view of membrane binding and complex formation of human
factor VIIa and tissue factor.
Y. Zenmei Ohkubo, James H. Morrissey, and Emad Tajkhorshid.
Journal of Thrombosis and Haemostasis, 8:1044-1053, 2010.
(PMC: PMC2890040) |
| 10040. Protein-phospholipid interactions in blood clotting.
James H. Morrissey, Rebecca L. Davis-Harrison, Narjes Tavoosi, Ke Ke, Vincent
Pureza, John M. Boettcher, Mary C. Clay, Chad M. Rienstra, Y. Zenmei Ohkubo,
Taras V. Pogorelov, and Emad Tajkhorshid.
Thrombosis Research, 125(Suppl. 1):S23-S25, 2010.
|
| 10041. Interplay of mechanical and binding properties of Fibronectin type
I.
Jiankuai Diao, Andrew J. Maniotis, Robert Folberg, and Emad Tajkhorshid.
Theoretica Chimica Acta, 125:397-405, 2010.
|
| 10038. Simulation of spontaneous substrate binding revealing the binding
pathway and mechanism and initial conformational response of GlpT.
Giray Enkavi and Emad Tajkhorshid.
Biochemistry, 49:1105-1114, 2010.
(PMC: 2829668) |
| 10045. Exploring transmembrane diffusion pathways with molecular dynamics.
Yi Wang, Saher A. Shaikh, and Emad Tajkhorshid.
Physiology, 25:142-154, 2010.
|
| 555. Implementation of accelerated molecular dynamics in NAMD.
Yi Wang, Chris B. Harrison, Klaus Schulten, and J. Andrew McCammon.
Computational Science & Discovery, 4:015002, 2011.
(PMC: PMC3115733) |
| 530. O2-reactivity of flavoproteins: Dynamic access of dioxygen to
the active site and role of a H+ relay system in D-amino acid oxidase.
Jan Saam, Elena Rosini, Gianluca Molla, Klaus Schulten, Loredano Pollegioni,
and Sandro Ghisla.
Journal of Biological Chemistry, 285:24439-24446, 2010.
(PMC: 2915680) |
| 531. Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic
membrane.
Jen Hsin, Johan Strümpfer, Melih Sener, Pu Qian, C. Neil Hunter, and Klaus
Schulten.
New Journal of Physics, 12:085005, 2010.
(19 pages).
(PMC: 2997751) |
| 527. Challenges in protein folding simulations.
Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten.
Nature Physics, 6:751-758, 2010.
(PMC: 3032381) |
| 529. Squeezing protein shells: how continuum elastic models, molecular
dynamics simulations and experiments coalesce at the nanoscale.
Wouter H. Roos, Melissa M. Gibbons, Anton Arkhipov, Charlotte Uetrecht, Norman
Watts, Paul Wingfield, Alasdair C. Steven, Albert J.R.Heck, Klaus Schulten,
William S. Klug, and Gijs J.L. Wuite.
Biophysical Journal, 99:1175-1181, 2010.
(PMC: 2920642) |
| 565. Cytoplasmic domain filter function in the mechanosensitive channel of
small conductance.
Ramya Gamini, Marcos Sotomayor, Christophe Chipot, and Klaus Schulten.
Biophysical Journal, 101:80-89, 2011.
(PMC: 3127185) |
| 526. Molecular dynamics simulations suggest that electrostatic funnel
directs binding of Tamiflu to influenza N1 neuraminidases.
Ly Le, Eric H. Lee, David J. Hardy, Thanh N. Truong, and Klaus Schulten.
PLoS Computational Biology, 6:e1000939, 2010.
(13 pages).
(PMC: 2944783) |
| 540. Fast molecular electrostatics algorithms on GPUs.
David J. Hardy, John E. Stone, Kirby L. Vandivort, David Gohara, Christopher
Rodrigues, and Klaus Schulten.
In Wen-mei Hwu, editor, GPU Computing Gems, chapter 4, pp.
43-58. Morgan Kaufmann Publishers, 2011.
|
| 539. GPU-accelerated computation and interactive display of molecular
orbitals.
John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus
Schulten.
In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pp.
5-18. Morgan Kaufmann Publishers, 2011.
|
| 532. Computational microscopy of the role of protonable surface residues
in nanoprecipitation oscillations.
Eduardo R. Cruz-Chu and Klaus Schulten.
ACS Nano, 4:4463-4474, 2010.
(PMC: 2927718) |
| 533. GPU-accelerated molecular modeling coming of age.
John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.
Journal of Molecular Graphics and Modelling, 29:116-125, 2010.
(PMC: 2934899) |
| 553. Cryo-EM structure of the ribosome-SecYE complex in the membrane
environment.
Jens Frauenfeld, James Gumbart, Eli O. van der Sluis, Soledad Funes, Marco
Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas
Becker, Klaus Schulten, and Roland Beckmann.
Nature Structural & Molecular Biology, 18:614-621, 2011.
(PMC: PMC3412285) |
| 521. Calculation of the gating charge for the Kv1.2 voltage-activated
potassium channel.
Fatemeh Khalili-Araghi, Vishwanath Jogini, Vladimir Yarov-Yarovoy, Emad
Tajkhorshid, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 98:2189-2198, 2010.
(PMC: 2872222) |
| 524. Photosynthetic vesicle architecture and constraints on efficient
energy harvesting.
Melih Sener, Johan Strumpfer, John A. Timney, Arvi Freiberg, C. Neil Hunter,
and Klaus Schulten.
Biophysical Journal, 99:67-75, 2010.
(PMC: 2895385) |
| 519. Self-assembly of photosynthetic membranes.
Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih
Sener, Johan Strumpfer, and Klaus Schulten.
ChemPhysChem, 11:1154-1159, 2010.
(PMC: 3086839) |
| 510. Science and engineering in the petascale era.
Thom H. Dunning Jr., Klaus Schulten, Jeroen Tromp, Jeremiah P. Ostriker, Kelvin
Droegemeier, Ming Xue, and Paul Fussell.
Computing in Science and Engineering, 11:28-36, 2009.
(PMC: 3190305) |
| 522. Going beyond clustering in MD trajectory analysis: an application
to villin headpiece folding.
Aruna Rajan, Peter L. Freddolino, and Klaus Schulten.
PLoS One, 5:e9890, 2010.
(12 pages).
(PMC: 2855342) |
| 520. Recognition of the regulatory nascent chain TnaC by the ribosome.
Leonardo G. Trabuco, Christopher B Harrison, Eduard Schreiner, and Klaus
Schulten.
Structure, 18:627-637, 2010.
(PMC: 3244694) |
| 523. Acuity of a cryptochrome and vision based magnetoreception system in
birds.
Ilia A. Solov'yov, Henrik Mouritsen, and Klaus Schulten.
Biophysical Journal, 99:40-49, 2010.
(PMC: 2895366) |
| 10037. Coupling of calcium and substrate binding through loop alignment in
the outer membrane transporter BtuB.
James Gumbart, Michael C. Wiener, and Emad Tajkhorshid.
Journal of Molecular Biology, 393:1129-1142, 2009.
(PMC: 2775145) |
| 514. Light harvesting complex II B850 excitation dynamics.
Johan Strümpfer and Klaus Schulten.
Journal of Chemical Physics, 131:225101, 2009.
(9 pages).
(PMC: 2802260) |
| 498. Molecular Dynamics Flexible Fitting: A practical guide to combine
cryo-electron microscopy and X-ray crystallography.
Leonardo G. Trabuco, Elizabeth Villa, Eduard Schreiner, Christopher B.
Harrison, and Klaus Schulten.
Methods, 49:174-180, 2009.
(PMC: 2753685) |
| 516. Tertiary and secondary structure elasticity of a six-Ig titin
chain.
Eric H. Lee, Jen Hsin, Eleonore von Castelmur, Olga Mayans, and Klaus Schulten.
Biophysical Journal, 98:1085-1095, 2010.
(PMC: 2849065) |
| 502. Ligand migration and cavities within scapharca dimeric HbI: Studies
by time-resolved crystallography, Xe binding, and computational analysis.
James E. Knapp, Reinhard Pahl, Jordi Cohen, Jeffry C. Nichols, Klaus Schulten,
Quentin H. Gibson, Vukica Srajer, and William E. Royer Jr.
Structure, 17:1494-1504, 2009.
(PMC: 2785043) |
| 508. Polarizable intermolecular potentials for water and benzene
interacting with halide and metal ions.
Fabien Archambault, Christophe Chipot, Ignacio Soteras, F. Javier Luque, Klaus
Schulten, and Francois Dehez.
Journal of Chemical Theory and Computation, 5:3022-3031, 2009.
(PMC: 2990227) |
| 500. Maturation of high-density lipoproteins.
Amy Y. Shih, Stephen G. Sligar, and Klaus Schulten.
Journal of the Royal Society Interface, 6:863-871, 2009.
(PMC: 2805102) |
| 518. Probing a structural model of the nuclear pore complex channel
through molecular dynamics.
Lingling Miao and Klaus Schulten.
Biophysical Journal, 98:1658-1667, 2010.
(PMC: 2865169) |
| 505. Membrane-bending mechanism of amphiphysin N-BAR domains.
Anton Arkhipov, Ying Yin, and Klaus Schulten.
Biophysical Journal, 97:2727-2735, 2009.
(PMC: 2776244) |
| 511. A glycophorin A-like framework for the dimerization of
photosynthetic core complexes.
Jen Hsin, Chris Chipot, and Klaus Schulten.
Journal of the American Chemical Society, 131:17096-17098,
2009.
(PMC: 2792896) |
| 512. Structure of monomeric yeast and mammalian Sec61 complexes
interacting with the translating ribosome.
Thomas Becker, Shashi Bhushan, Alexander Jarasch, Jean-Paul Armache, Soledad
Funes, Fabrice Jossinet, James Gumbart, Thorsten Mielke, Otto Berninghausen,
Klaus Schulten, Eric Westhof, Reid Gilmore, Elisabet C. Mandon, and Roland
Beckmann.
Science, 326:1369-1373, 2009.
(PMC: 2920595) |
| 513. Structural insight into nascent polypeptide chain-mediated
translational stalling.
Birgit Seidelt, C. Axel Innis, Daniel N. Wilson, Marco Gartmann, Jean-Paul
Armache, Elizabeth Villa, Leonardo G. Trabuco, Thomas Becker, Thorsten
Mielke, Klaus Schulten, Thomas A. Steitz, and Roland Beckmann.
Science, 326:1412-1415, 2009.
(PMC: 2920484) |
| 506. Discovery through the computational microscope.
Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, and Klaus Schulten.
Structure, 17:1295-1306, 2009.
(PMC: 2927212) |
| 515. Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and
avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza.
Ly Le, Eric H. Lee, Klaus Schulten, and Thahn Truong.
PLoS Currents: Influenza, 2009 Aug 27:RRN1015, 2010.
(9 pages).
(PMC: 2762416) |
| 509. Regulation of the protein-conducting channel by a bound ribosome.
James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and
Klaus Schulten.
Structure, 17:1453-1464, 2009.
(PMC: 2778611) |
| 10035. Structural and functional analysis of SoPIP2;1 mutants add insight
into plant aquaporin gating.
Maria Nyblom, Anna Frick, Yi Wang, Mikael Ekvall, Karin Hallgren, Kristina
Hedfalk, Richard Neutze, Emad Tajkhorshid, and Susanna
Törnroth-Horsefield.
Journal of Molecular Biology, 387:653-668, 2009.
|
| 503. Elucidating the mechanism behind irreversible deformation of viral
capsids.
Anton Arkhipov, Wouter H. Roos, Gijs J. L. Wuite, and Klaus Schulten.
Biophysical Journal, 97:2061-2069, 2009.
(PMC: 2756377) |
| 517. Multi-scale simulations of membrane sculpting by N-BAR domains.
Ying Yin, Anton Arkhipov, and Klaus Schulten.
In Philip Biggin and Mark Sansom, editors, Molecular Simulations
and Biomembranes: From Biophysics to Function, chapter 6, pp. 146-176.
Royal Society of Chemistry, 2010.
|
| 501. Molecular control of ionic conduction in polymer nanopores.
Eduardo R. Cruz-Chu, Thorsten Ritz, Zuzanna S. Siwy, and Klaus Schulten.
Faraday Discussions, 143:47-62, 2009.
(PMC: 2907245) |
| 504. Common structural transitions in explicit-solvent simulations of
villin headpiece folding.
Peter L. Freddolino and Klaus Schulten.
Biophysical Journal, 97:2338-2347, 2009.
(PMC: 2764099) |
| 10039. Long time-scale simulations of in vivo diffusion using GPU
hardware.
Elijah Roberts, John E. Stone, Leonardo Sepulveda, Wen-mei W. Hwu, and Zaida
Luthey-Schulten.
In Proceedings of the IEEE International Parallel &
Distributed Processing Symposium, pp. 1-8, 2009.
|
| 499. Protein-induced membrane curvature investigated through molecular
dynamics flexible fitting.
Jen Hsin, James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil
Hunter, and Klaus Schulten.
Biophysical Journal, 97:321-329, 2009.
(PMC: 2711417) |
| 10033. Potential cation and H+ binding sites in acid sensing ion
channel-1.
S. A. Shaikh and E. Tajkhorshid.
Biophysical Journal, 95:5153-5164, 2008.
(PMC: 2586576) |
| 10034. Dimer opening of the nucleotide binding domains of ABC transporters
after ATP hydrolysis.
P.-C. Wen and E. Tajkhorshid.
Biophysical Journal, 95:5100-5110, 2008.
(PMC: 2586561) |
| 507. Membrane curvature induced by aggregates of LH2s and monomeric
LH1s.
Danielle E. Chandler, James Gumbart, John D. Stack, Christophe Chipot, and
Klaus Schulten.
Biophysical Journal, 97:2978-2984, 2009.
(PMC: 2784572) |
| 495. Molecular dynamics simulations of membrane channels and transporters.
Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad
Tajkhorshid, and Klaus Schulten.
Current Opinion in Structural Biology, 19:128-137, 2009.
(PMC: 2680122) |
| 492. High performance computation and interactive display of molecular
orbitals on GPUs and multi-core CPUs.
John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu,
and Klaus Schulten.
In Proceedings of the 2nd Workshop on General-Purpose Processing
on Graphics Processing Units, ACM International Conference Proceeding
Series, volume 383, pp. 9-18, New York, NY, USA, 2009. ACM.
|
| 497. Magnetoreception through cryptochrome may involve superoxide.
Ilia A. Solov'yov and Klaus Schulten.
Biophysical Journal, 96:4804-4813, 2009.
(PMC: 2712043) |
| 10031. Self-assembly route for embedding polyoxomolybdate capsules in lipid
bilayer membranes.
R. Carr, I. A. Weinstock, A. Sivaprasadarao, A. Müller, and A. Aksimentiev.
Nano Letters, 8:3916-3921, 2008.
|
| 10030. Strain softening in stretched DNA.
B. Luan and A. Aksimentiev.
Physical Review Letters, 101:118101, 2008.
|
| 10029. Electro-osmotic screening of the DNA charge in a nanopore.
B. Luan and A. Aksimentiev.
Physical Review E, 78:021912, 2008.
|
| 10032. DNA attraction in mono- and divalent electrolytes.
B. Luan and A. Aksimentiev.
Journal of the American Chemical Society, 130:15754-15755,
2008.
|
| 494. Force field bias in protein folding simulations.
Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 96:3772-3780, 2009.
(PMC: 2711430) |
| |
| 484. Nanoelectromechanics of methylated DNA in a synthetic nanopore.
Utkur M. Mirsaidov, Winston Timp, Xueqing Zou, Valentin Dimitrov, Klaus
Schulten, Andrew P. Feinberg, and Greg Timp.
Biophysical Journal, 96:L32-L34, 2009.
(PMC: 2717226) |
| 491. Structural model and excitonic properties of the dimeric
RC-LH1-PufX complex from Rhodobacter sphaeroides.
Melih K. Sener, Jen Hsin, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian,
C. Neil Hunter, and Klaus Schulten.
Chemical Physics, 357:188-197, 2009.
(PMC: 2678753) |
| 488. Modeling transport through synthetic nanopores.
Aleksei Aksimentiev, Robert K. Brunner, Eduardo Cruz-Chu, Jeffrey Comer, and
Klaus Schulten.
IEEE Nanotechnology, 3:20-28, 2009.
(PMC: 3168529) |
| 481. Adapting a message-driven parallel application to GPU-accelerated
clusters.
James C. Phillips, John E. Stone, and Klaus Schulten.
In SC '08: Proceedings of the 2008 ACM/IEEE Conference on
Supercomputing, Piscataway, NJ, USA, 2008. IEEE Press.
(9 pages).
|
| 10027. Dynamics of the extracellular gate and ion-substrate coupling in the
glutamate transporter.
Zhijian Huang and Emad Tajkhorshid.
Biophysical Journal, 95:2292-2300, 2008.
(PMC: 2517027) |
| 487. Ribosome-induced changes in elongation factor Tu conformation
control GTP hydrolysis.
Elizabeth Villa, Jayati Sengupta, Leonardo G. Trabuco, Jamie LeBarron,
William T. Baxter, Tanvir R. Shaikh, Robert A. Grassucci, Poul Nissen,
Måns Ehrenberg, Klaus Schulten, and Joachim Frank.
Proceedings of the National Academy of Sciences, USA,
106:1063-1068, 2009.
(PMC: 2613361) |
| 496. Simulations of membrane tubulation by lattices of amphiphysin N-BAR
domains.
Ying Yin, Anton Arkhipov, and Klaus Schulten.
Structure, 17:882-892, 2009.
(PMC: 2743466) |
| 493. Limits for reduction of effective focal volume in multiple-beam light
microscopy.
Anton Arkhipov and Klaus Schulten.
Optics Express, 17:2861-2870, 2009.
(PMC: 3160275) |
| 479. Molecular mechanisms of ligand recognition by NR3 subtype glutamate
receptors.
Yongneng Yao, Christopher B. Harrison, Peter L. Freddolino, Klaus Schulten, and
Mark L. Mayer.
EMBO Journal, 27:2158-2170, 2008.
(PMC: 2516888) |
| 10026. Electrostatic funneling of substrate in mitochondrial inner membrane
carriers.
Yi Wang and Emad Tajkhorshid.
Proceedings of the National Academy of Sciences, USA,
105:9598-9603, 2008.
(PMC: 2474497) |
| 486. Multilevel summation of electrostatic potentials using graphics
processing units.
David J. Hardy, John E. Stone, and Klaus Schulten.
Journal of Parallel Computing, 35:164-177, 2009.
(PMC: 2743154) |
| 483. Photochemical reaction dynamics of the primary event of vision
studied by a hybrid molecular simulation.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 96:403-416, 2009.
(PMC: 19167292) |
| 490. Transport-related structures and processes of the nuclear pore
complex studied through molecular dynamics.
Lingling Miao and Klaus Schulten.
Structure, 17:449-459, 2009.
(PMC: 2701619) |
| 485. Ionic current rectification through silica nanopores.
Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten.
Journal of Physical Chemistry C, 113:1850-1862, 2009.
(PMC: 2658614) |
| 489. Elasticity and rupture of a multi-domain neural cell adhesion
molecule complex.
Venkat Maruthamuthu, Klaus Schulten, and Deborah Leckband.
Biophysical Journal, 96:3005-3014, 2009.
(PMC: 2718298) |
| 476. The roles of pore ring and plug in the SecY protein-conducting
channel.
James Gumbart and Klaus Schulten.
Journal of General Physiology, 132:709-719, 2008.
(PMC: 2585858) |
| 482. Using VMD - an introductory tutorial.
Jen Hsin, Anton Arkhipov, Ying Yin, John E. Stone, and Klaus Schulten.
Current Protocols - Bioinformatics, 5:Unit 5.7, 2008.
(48 pages).
(PMC: 2972669) |
| 475. Exploring the possibilities for radical pair effects in cryptochrome.
Ilia A. Solov'yov, Danielle Chandler, and Klaus Schulten.
Plant Signaling and Behavior, 3:676-677, 2008.
(PMC: 2634554) |
| 480. A structural mechanism for MscS gating in lipid bilayers.
Valeria Vasquez, Marcos Sotomayor, Julio Cordero-Morales, Klaus Schulten, and
Eduardo Perozo.
Science, 321:1210-1214, 2008.
(PMC: 2897165) |
| 471. From atomic-level structure to supramolecular organization in the
photosynthetic unit of purple bacteria.
Melih K. Sener and Klaus Schulten.
In C. Neil Hunter, Fevzi Daldal, Marion C. Thurnauer, and J. Thomas
Beatty, editors, The Purple Phototrophic Bacteria, volume 28 of
Advances in Photosynthesis and Respiration, pp. 275-294. Springer, 2008.
|
| 10023. Indirect role of Ca2+ in the assembly of extracelluar matrix
proteins.
Jiankuai Diao and Emad Tajkhorshid.
Biophysical Journal, 95:120-127, 2008.
(PMC: 2426659) |
| 10022. Gas conduction of lipid bilayers and membrane channels.
Y. Wang, Y. Zenmei Ohkubo, and E. Tajkhorshid.
In Scott Feller, editor, Current Topics in Membranes:
Computational Modeling of Membrane Bilayers, volume 60, chapter 12, pp.
343-367. Elsevier, 2008.
|
| 10025. Resolution enhancement in solid-state NMR spectra of oriented
membrane proteins by anisotropic differential linebroadening.
T. Vosegaard, K. Bertelsen, J. M. Pedresen, L. Thøgersen, B. Schiøtt,
E. Tajkhorshid, T Skrydstrup, and N. Chr. Nielsen.
Journal of the American Chemical Society, 130:5028-5029, 2008.
|
| 10024. Blood clotting reactions on nanoscale phospholipid bilayers.
J. H. Morrissey, V. Pureza, R. L. Davis-Harrison, S. G. Sligar, Y. Z. Ohkubo,
and E. Tajkhorshid.
Thrombosis Research, 122:S23-S26, 2008.
|
| 477. Intrinsic curvature properties of photosynthetic proteins in
chromatophores.
Danielle Chandler, Jen Hsin, Christopher B. Harrison, James Gumbart, and Klaus
Schulten.
Biophysical Journal, 95:2822-2836, 2008.
(PMC: 2527265) |
| 474. Flow induced structural transition in the β-switch region of
glycoprotein Ib.
Zhongzhou Chen, Jizhong Lou, Cheng Zhu, and Klaus Schulten.
Biophysical Journal, 95:1303-1313, 2008.
(PMC: 2479615) |
| 478. Four-scale description of membrane sculpting by BAR domains.
Anton Arkhipov, Ying Yin, and Klaus Schulten.
Biophysical Journal, 95:2806-2821, 2008.
(PMC: 2527247) |
| 10021. Scalable molecular dynamics with NAMD on the IBM Blue
Gene/L system.
S. Kumar, C. Huang, G. Zheng, E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, and
L. V. Kale.
IBM Journal of Research and Development, 52:177-188, 2008.
|
| 10020. GPU computing.
John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and
James C. Phillips.
Proceedings of the IEEE, 96:879-899, 2008.
|
| 469. Ten-microsecond molecular dynamics simulation of a fast-folding WW
domain.
Peter L. Freddolino, Feng Liu, Martin Gruebele, and Klaus Schulten.
Biophysical Journal, 94:L75-L77, 2008.
(PMC: 2367204) |
| 468. GPU acceleration of cutoff pair potentials for molecular modeling
applications.
Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and
Wen-mei W. Hwu.
In CF'08: Proceedings of the 2008 conference on Computing
Frontiers, pp. 273-282, New York, NY, USA, 2008. ACM.
|
| 472. Molecular models need to be tested: the case of a solar flares
discoidal HDL model.
Amy Y. Shih, Stephen G. Sligar, and Klaus Schulten.
Biophysical Journal, 94:L87-L89, 2008.
(PMC: 2397337) |
| 473. Flexible fitting of atomic structures into electron microscopy maps
using molecular dynamics.
Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and Klaus
Schulten.
Structure, 16:673-683, 2008.
(PMC: 2430731) |
| 470. Mechanism of signal propagation upon retinal isomerization: Insights
from molecular dynamics simulations of rhodopsin restrained by normal modes.
Basak Isin, Klaus Schulten, Emad Tajkhorshid, and Ivet Bahar.
Biophysical Journal, 95:789-803, 2008.
(PMC: 2440475) |
| 464. Understanding structure and function of membrane proteins using free
energy calculations.
Christophe Chipot and Klaus Schulten.
In Eva Pebay-Peyroula, editor, Biophysical analysis of membrane
proteins. Investigating structure and function, pp. 187-211. Wiley,
Weinheim, 2008.
|
| 10014. Substrate binding and formation of an occluded state in the leucine
transporter.
L. Celik, B. Schiott, and E. Tajkhorshid.
Biophysical Journal, 94:1600-1612, 2008.
(PMC: 2242742) |
| 10016. Exploring transmembrane transport through α-hemolysin with
grid-steered molecular dynamics.
David B. Wells, Volha Abramkina, and Aleksei Aksimentiev.
Journal of Chemical Physics, 127:125101, 2007.
|
| 10015. Structure refinement of the OpcA adhesin using molecular dynamics.
Binquan Luan, Martin Caffrey, and Aleksei Aksimentiev.
Biophysical Journal, 93:3058-3069, 2007.
(PMC: 2025660) |
| 10018. Stretching and unzipping nucleic acid hairpins using a synthetic
nanopore.
Q. Zhao, J. Comer, S. Yemenicioglu, A. Aksimentiev, and G. Timp.
Nucleic Acids Research, 36:1532-1541, 2008.
(PMC: 2275135) |
| 10019. Detection of DNA sequences using an alternating electric field in a
nanopore capacitor.
G. Sigalov, J. Comer, G. Timp, and A. Aksimentiev.
Nano Letters, 8:56-63, 2008.
(PMC: 2588427) |
| 10017. In meso crystal structure and computer simulations suggest an
alternative proteoglycan binding site in the OpcA outer membrane adhesin.
V. Cherezov, W. Liu, J. Derrick, B. Luan, A. Aksimentiev, V. Katruc, and
M. Caffrey.
PROTEINS: Structure, Function, and Bioinformatics, 71:24-34,
2008.
|
| 10013. Distinct structural and adhesive roles of Ca2+ in membrane
binding of blood coagulation factors.
Y. Zenmei Ohkubo and Emad Tajkhorshid.
Structure, 16:72-81, 2008.
|
| 467. The allosteric role of the Ca++ switch in adhesion and
elasticity of C-cadherin.
Marcos Sotomayor and Klaus Schulten.
Biophysical Journal, 94:4621-4633, 2008.
(PMC: 2397358) |
| 462. Molecular modeling of the structural properties and formation of
high-density lipoprotein particles.
Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, Stephen G. Sligar, and Klaus
Schulten.
In Scott Feller, editor, Current Topics in Membranes:
Computational Modeling of Membrane Bilayers, chapter 11, pp. 313-342.
Elsevier, 2008.
|
| 461. Application of residue-based and shape-based coarse graining to
biomolecular simulations.
Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and
Klaus Schulten.
In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase
and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC
Press, Taylor and Francis Group, 2008.
|
| 466. Length dependent optical effects in single walled carbon nanotubes.
Aruna Rajan, Michael S. Strano, Daniel A. Heller, Tobias Hertel, and Klaus
Schulten.
Journal of Physical Chemistry B, 112:6211-6213, 2008.
|
| 451. Double stranded DNA dissociates into single strands when dragged
into a poor solvent.
Shuxun Cui, Jin Yu, Ferdinand Kühner, Klaus Schulten, and Hermann E. Gaub.
Journal of the American Chemical Society, 129:14710-14716,
2007.
|
| 454. Modeling induction phenomena in intermolecular interactions with an
ab initio force field.
Francois Dehez, Janos G. Angyan, Ignacio Soteras Gutierrez, F. Javier Luque,
Klaus Schulten, and Christophe Chipot.
Journal of Chemical Theory and Computation, 3:1914-1926, 2007.
|
| 460. Finding gas migration pathways in proteins using implicit ligand
sampling.
Jordi Cohen, Kenneth W. Olsen, and Klaus Schulten.
In Robert K. Poole, editor, Globins and other NO-reactive
Proteins in Microbes, Plants and Invertebrates, volume 437 of Methods
in Enzymology, pp. 437-455. Elsevier, 2008.
|
| 465. Molecular basis of fibrin clot elasticity.
Bernard Lim, Eric H. Lee, Marcos Sotomayor, and Klaus Schulten.
Structure, 16:449-459, 2008.
|
| 463. Three dimensional architecture of membrane-embedded MscS in the
closed conformation.
Valeria Vasquez, Marcos Sotomayor, D. Marien Cortes, Benoit Roux, Klaus
Schulten, and Eduardo Perozo.
Journal of Molecular Biology, 378:55-70, 2008.
(PMC: 2703500) |
| 432. Fluorescence-force spectroscopy maps two-dimensional reaction
landscape of the Holliday junction.
Sungchul Hohng, Ruobo Zhou, Michelle K. Nahas, Jin Yu, Klaus Schulten, David
M. J. Lilley, and Taekjip Ha.
Science, 318:279-283, 2007.
|
| 457. Computer modeling in biotechnology, a partner in development.
Aleksei Aksimentiev, Robert Brunner, Jordi Cohen, Jeffrey Comer, Eduardo
Cruz-Chu, David Hardy, Aruna Rajan, Amy Shih, Grigori Sigalov, Ying Yin, and
Klaus Schulten.
In Protocols in Nanostructure Design, Methods in Molecular
Biology, pp. 181-234. Humana Press, 2008.
|
| 458. Diffusion of glycerol through Escherichia coli
aquaglyceroporin GlpF.
Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot.
Biophysical Journal, 94:832-839, 2008.
(PMC: 2186255) |
| 10012. Molecular mechanisms of conduction and selectivity in aquaporin water
channels.
Yi Wang and Emad Tajkhorshid.
Journal of Nutrition, 137:1509S-1515S, 2007.
|
| 459. Biomolecular modeling in the era of petascale computing.
Klaus Schulten, James C. Phillips, Laxmikant V. Kalé, and Abhinav Bhatele.
In David Bader, editor, Petascale Computing: Algorithms and
Applications, pp. 165-181. Chapman and Hall/CRC Press, Taylor and Francis
Group, New York, 2008.
|
| 446. Cse1p binding dynamics reveal a novel binding pattern for FG-repeat
nucleoporins on transport receptors.
Timothy A. Isgro and Klaus Schulten.
Structure, 15:977-991, 2007.
|
| 10011. Detecting SNPs using a synthetic nanopore.
Q. Zhao, G. Sigalov, V. Dimitrov, B. Dorvel, U. Mirsaidov, S. Sligar,
A. Aksimentiev, and G. Timp.
Nano Letters, 7:1680-1685, 2007.
(PMC: 2565804) |
| 453. Accelerating molecular modeling applications with graphics
processors.
John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy,
Leonardo G. Trabuco, and Klaus Schulten.
Journal of Computational Chemistry, 28:2618-2640, 2007.
|
| 448. How directional translocation is regulated in a DNA helicase motor.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Biophysical Journal, 93:3783-3797, 2007.
(PMC: 2084242) |
| 10010. Mechanics of force propagation in TonB-dependent outer membrane
transport.
James Gumbart, Michael C. Wiener, and Emad Tajkhorshid.
Biophysical Journal, 93:496-504, 2007.
(PMC: 1896255) |
| 445. Disassembly of nanodiscs with cholate.
Amy Y. Shih, Peter L. Freddolino, Stephen G. Sligar, and Klaus Schulten.
Nano Letters, 7:1692-1696, 2007.
|
| 444. Single-molecule experiments in vitro and in silico.
Marcos Sotomayor and Klaus Schulten.
Science, 316:1144-1148, 2007.
|
| 455. Atomic level structural and functional model of a bacterial
photosynthetic membrane vesicle.
Melih K. Sener, John D. Olsen, C. Neil Hunter, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
104:15723-15728, 2007.
(PMC: 2000399) |
| 452. Continuous fluorescence microphotolysis and correlation spectroscopy
using 4Pi microscopy.
Anton Arkhipov, Jana Hüve, Martin Kahms, Reiner Peters, and Klaus Schulten.
Biophysical Journal, 93:4006-4017, 2007.
(PMC: 2084225) |
| 442. Exploring molecular oxygen pathways in Hanseluna Polymorpha
copper-containing amine oxidase.
Bryan J. Johnson, Jordi Cohen, Richard W. Welford, Arwen R. Pearson, Klaus
Schulten, Judith P. Klinman, and Carrie M. Wilmot.
Journal of Biological Chemistry, 282:17767-17776, 2007.
(PMC: 3081669) |
| 443. Secondary and tertiary structure elasticity of titin Z1Z2 and a
titin chain model.
Eric H. Lee, Jen Hsin, Olga Mayans, and Klaus Schulten.
Biophysical Journal, 93:1719-1735, 2007.
(PMC: 1948054) |
| 450. Structural determinants of lateral gate opening in the protein
translocon.
James Gumbart and Klaus Schulten.
Biochemistry, 46:11147-11157, 2007.
|
| 441. Sugar transport across lactose permease probed by steered molecular
dynamics.
Morten Ø. Jensen, Ying Yin, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 93:92-102, 2007.
(PMC: 1914442) |
| 447. Assembly of lipids and proteins into lipoprotein particles.
Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, Stephen G. Sligar, and Klaus
Schulten.
Journal of Physical Chemistry B, 111:11095-11104, 2007.
|
| 449. O2 migration pathways are not conserved across proteins of a
similar fold.
Jordi Cohen and Klaus Schulten.
Biophysical Journal, 93:3591-3600, 2007.
(PMC: 2072066) |
| 440. Magnetic field effects in Arabidopsis thaliana cryptochrome-1.
Ilia A. Solov'yov, Danielle E. Chandler, and Klaus Schulten.
Biophysical Journal, 92:2711-2726, 2007.
(PMC: 1831705) |
| 439. Association of nuclear pore FG-repeat domains to NTF2 import and
export complexes.
Timothy A. Isgro and Klaus Schulten.
Journal of Molecular Biology, 366:330-345, 2007.
|
| 437. Ion conduction through MscS as determined by electrophysiology and
simulation.
Marcos Sotomayor, Valeria Vasquez, Eduardo Perozo, and Klaus Schulten.
Biophysical Journal, 92:886-902, 2007.
(PMC: 1779981) |
| 436. Exploring gas permeability of cellular membranes and membrane
channels with molecular dynamics.
Yi Wang, Jordi Cohen, Walter F. Boron, Klaus Schulten, and Emad Tajkhorshid.
Journal of Structural Biology, 157:534-544, 2007.
|
| 428. Structural and functional investigations of biological catalysts for
optimization of solar-driven, H2 production systems.
Paul W. King, Drazenka Svedruzic, Jordi Cohen, Klaus Schulten, Michael Seibert,
and Maria L. Ghirardi.
In Lionel Vayssieres, editor, Solar Hydrogen and
Nanotechnology, volume 6340 of Proceedings of the Society of
Photo-Optical Instrumentation Engineers, pp. 259-267, 2006.
|
| 427. [FeFe]-hydrogenases and photobiological hydrogen production.
Maria L. Ghirardi, Jordi Cohen, Paul King, Klaus Schulten, Kwiseon Kim, and
Michael Seibert.
In Lionel Vayssieres, editor, Solar hydrogen and
Nanotechnology, volume 6340 of Proceedings of the Society of
Photo-Optical Instrumentation Engineers, pp. 253-258, 2006.
|
| 417. Coarse-grained molecular dynamics simulations of a rotating bacterial
flagellum.
Anton Arkhipov, Peter L. Freddolino, Katsumi Imada, Keiichi Namba, and Klaus
Schulten.
Biophysical Journal, 91:4589-4597, 2006.
(PMC: 1779929) |
| 429. Stability and dynamics of virus capsids described by coarse-grained
modeling.
Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten.
Structure, 14:1767-1777, 2006.
|
| 424. Dynamics of K+ ion conduction through Kv1.2.
Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 91:L72-L74, 2006.
(PMC: 1557577) |
| 414. Water-silica force field for simulating nanodevices.
Eduardo R. Cruz-Chu, Aleksei Aksimentiev, and Klaus Schulten.
Journal of Physical Chemistry B, 110:21497-21508, 2006.
(PMC: 2517990) |
| 435. Charge delocalization in proton channels. I. The aquaporin
channels and proton blockage.
Hanning Chen, Boaz Ilan, Yujie Wu, Fangqiang Zhu, Klaus Schulten, and
Gregory A. Voth.
Biophysical Journal, 92:46-60, 2007.
(PMC: 1697834) |
| 430. How the headpiece hinge angle is opened: new insights into the
dynamics of integrin activation.
Eileen Puklin-Faucher, Mu Gao, Klaus Schulten, and Viola Vogel.
Journal of Cell Biology, 175:349-360, 2006.
(PMC: 2064575) |
| 410. Molecular dynamics studies of the archaeal translocon.
James Gumbart and Klaus Schulten.
Biophysical Journal, 90:2356-2367, 2006.
(PMC: 1403164) |
| 425. Mechanism of gating and ion conductivity of a possible tetrameric
pore in Aquaporin-1.
Jin Yu, Andrea J. Yool, Klaus Schulten, and Emad Tajkhorshid.
Structure, 14:1411-1423, 2006.
|
| 438. Assembly of lipoprotein particles revealed by coarse-grained
molecular dynamics simulations.
Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten.
Journal of Structural Biology, 157:579-592, 2007.
|
| 433. Molecular dynamics methods for bioelectronic systems in
photosynthesis.
Ioan Kosztin and Klaus Schulten.
In Thijs Aartsma and Joerg Matysik, editors, Biophysical
Techniques in Photosynthesis II, volume 26 of Advances in
Photosynthesis and Respiration, pp. 445-464. Springer, Dordrecht, 2008.
|
| 416. Molecular dynamics study of MscL interactions with a curved lipid
bilayer.
Grischa Raphael Meyer, Justin Gullingsrud, Klaus Schulten, and Boris Martinac.
Biophysical Journal, 91:1630-1637, 2006.
(PMC: 1544281) |
| 418. PcrA helicase, a molecular motor studied from the electronic to the
functional level.
Markus Dittrich, Jin Yu, and Klaus Schulten.
Topics in Current Chemistry, 268:319-347, 2006.
|
| 426. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant
phototropins.
Peter L. Freddolino, Markus Dittrich, and Klaus Schulten.
Biophysical Journal, 91:3630-3639, 2006.
(PMC: 1630464) |
| 456. Managing biomolecular simulations in a grid environment with
NAMD-G.
Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus
Schulten.
In Proceedings of the 2006 TeraGrid Conference, 2006.
(7 pages).
|
| 10009. Electrical signatures of single-stranded DNA with single base
mutations in a nanopore capacitor.
Maria E. Gracheva, Aleksei Aksimentiev, and Jean-Pierre Leburton.
Nanotechnology, 17:3160-3165, 2006.
|
| 422. PcrA helicase, a prototype ATP-driven molecular motor.
Markus Dittrich and Klaus Schulten.
Structure, 14:1345-1353, 2006.
|
| 420. Structure-based model of the stepping motor of PcrA helicase.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Biophysical Journal, 91:2097-2114, 2006.
(PMC: 1557568) |
| 419. Molecular mechanisms of cellular mechanics.
Mu Gao, Marcos Sotomayor, Elizabeth Villa, Eric Lee, and Klaus Schulten.
Physical Chemistry - Chemical Physics, 8:3692-3706, 2006.
|
| 421. Color tuning in rhodopsins: the mechanism for the spectral shift
between bacteriorhodopsin and sensory rhodopsin II.
Michael Hoffmann, Marius Wanko, Paul Strodel, Peter H. Koenig, Thomas
Frauenheim, Klaus Schulten, Walter Thiel, Emad Tajkhorshid, and Marcus
Elstner.
Journal of the American Chemical Society, 128:10808-10818,
2006.
|
| 431. Sugar binding and protein conformational changes in lactose permease.
Ying Yin, Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 91:3972-3985, 2006.
(PMC: 1635680) |
| 411. Modeling DNA loops using the theory of elasticity.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Physical Review E, 73:031919, 2006.
(23 pages).
|
| 434. Possible pathway for ubiquinone shuttling in R. rubrum
revealed by molecular dynamics simulation.
Andrew Aird, Jörg Wrachtrup, Klaus Schulten, and Carsten Tietz.
Biophysical Journal, 92:23-33, 2007.
(PMC: 1697858) |
| 409. Mechanical strength of the titin Z1Z2/telethonin complex.
Eric H. Lee, Mu Gao, Nikos Pinotsis, Matthias Wilmanns, and Klaus Schulten.
Structure, 14:497-509, 2006.
|
| 405. Coarse grained protein-lipid model with application to lipoprotein
particles.
Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten.
Journal of Physical Chemistry B, 110:3674-3684, 2006.
(PMC: 2535944) |
| 413. Electrostatic properties of the mechanosensitive channel of small
conductance MscS.
Marcos Sotomayor, Trudy A. van der Straaten, Umberto Ravaioli, and Klaus
Schulten.
Biophysical Journal, 90:3496-3510, 2006.
(PMC: 1440732) |
| 415. Imaging the migration pathways for O2, CO, NO, and Xe
inside myoglobin.
Jordi Cohen, Anton Arkhipov, Rosemary Braun, and Klaus Schulten.
Biophysical Journal, 91:1844-1857, 2006.
(PMC: 1544290) |
| 404. The electromechanics of DNA in a synthetic nanopore.
J. B. Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar,
K. Schulten, and G. Timp.
Biophysical Journal, 90:1098-1106, 2006.
(PMC: 1367096) |
| 412. Onset of anthrax toxin pore formation.
Mu Gao and Klaus Schulten.
Biophysical Journal, 90:3267-3279, 2006.
(PMC: 1432108) |
| 10007. Towards theoretical analysis of long-range proton transfer kinetics
in biomolecular pumps.
P. H. Koenig, N. Ghosh, M. Hoffmann, M. Elstner, E. Tajkhorshid, Th.
Frauenheim, and Q. Cui.
Journal of Physical Chemistry A, 110:548-563, 2006.
(PMC: 2728601) |
| 423. Conformational equilibrium in alanine-rich peptides probed by
reversible stretching simulations.
Jerome Henin, Klaus Schulten, and Christophe Chipot.
Journal of Physical Chemistry B, 110:16718-16723, 2006.
|
| 407. Simulation of the electric response of DNA translocation through a
semiconductor nanopore-capacitor.
Maria E. Gracheva, Anlin Xiong, Aleksei Aksimentiev, Klaus Schulten, Gregory
Timp, and Jean-Pierre Leburton.
Nanotechnology, 17:622-633, 2006.
|
| 10006. Receptive field and feature map formation in the primary visual
cortex via hebbian learning with inhibitory feedback.
Ted Hesselroth and Klaus Schulten.
arXiv:q-bio.NC/0505011v1, 2005.
|
| 10008. Structural mechanism of plant aquaporin gating.
S. Törnroth-Horsefield, Y. Wang, K. Hedfalk, U. Johanson, M. Karlsson,
E. Tajkhorshid, R. Neutze, and P. Kjellbom.
Nature, 439:688-694, 2006.
|
| 10005. The dynamics of image processing by feature maps in the primary
visual cortex.
Ted Hesselroth and Klaus Schulten.
arXiv:q-bio.NC/0505010v1, 2005.
|
| 389. In search of the hair-cell gating spring: Elastic properties of
ankyrin and cadherin repeats.
Marcos Sotomayor, David P. Corey, and Klaus Schulten.
Structure, 13:669-682, 2005.
|
| 391. Stretching DNA using an electric field in a synthetic nanopore.
J. B Heng, A. Aksimentiev, C. Ho, P. Marks, Y. V. Grinkova, S. Sligar,
K. Schulten, and G. Timp.
Nano Letters, 5:1883-1888, 2005.
(PMC: 2441849) |
| 381. Towards understanding membrane channels.
Emad Tajkhorshid, Jordi Cohen, Aleksij Aksimentiev, Marcos Sotomayor, and Klaus
Schulten.
In Boris Martinac and Andrzej Kubalski, editors, Bacterial ion
channels and their eukaryotic homologues, pp. 153-190. ASM Press,
Washington, DC, 2005.
|
| 400. Scalable molecular dynamics with NAMD.
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid,
Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and
Klaus Schulten.
Journal of Computational Chemistry, 26:1781-1802, 2005.
(PMC: 2486339)) |
| 393. When light falls in LOV: A quantum mechanical/molecular mechanical
study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii.
Markus Dittrich, Peter L. Freddolino, and Klaus Schulten.
Journal of Physical Chemistry B, 109:13006-13013, 2005.
(PMC: 2453334) |
| 387. Imaging alpha-hemolysin with molecular dynamics: Ionic conductance,
osmotic permeability and the electrostatic potential map.
Aleksij Aksimentiev and Klaus Schulten.
Biophysical Journal, 88:3745-3761, 2005.
(PMC: 1305609) |
| 395. Beyond the gene chip.
J. B. Heng, A. Aksimentiev, C. Ho, V. Dimitrov, T. Sorsch, J. Miner,
W. Mansfield, K. Schulten, and G. Timp.
Bell Labs Technical Journal, 10:5-22, 2005.
|
| 385. Molecular dynamics and experimental investigation of H2 and
O2 diffusion in [Fe]-hydrogenase.
Jordi Cohen, Kwiseon Kim, Matthew Posewitz, Maria L. Ghirardi, Klaus Schulten,
Michael Seibert, and Paul King.
Biochemical Society Transactions, 33:80-82, 2005.
(PMC: 2587414) |
| 397. Molecular dynamics simulations of proteins in lipid bilayers.
James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus
Schulten.
Current Opinion in Structural Biology, 15:423-431, 2005.
(PMC: 2474857) |
| 401. Binding dynamics of isolated nucleoporin repeat regions to
importin-β.
Timothy A. Isgro and Klaus Schulten.
Structure, 13:1869-1879, 2005.
|
| 383. Screening of water dipoles inside finite-length armchair carbon
nanotubes.
Yan Li, Deyu Lu, Slava V. Rotkin, Klaus Schulten, and Umberto Ravaioli.
Journal of Computational Electronics, 4:161-165, 2005.
(PMC: 2572853) |
| 406. Molecular dynamics simulations of the complete satellite tobacco
mosaic virus.
Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson,
and Klaus Schulten.
Structure, 14:437-449, 2006.
|
| 390. Empirical nanotube model for biological applications.
Deyu Lu, Yan Li, Umberto Ravaioli, and Klaus Schulten.
Journal of Physical Chemistry B, 109:11461-11467, 2005.
(PMC: 2441848) |
| 408. The role of molecular modeling in bionanotechnology.
Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L.
Freddolino, Anton Arkhipov, and Klaus Schulten.
Physical Biology, 3:S40-S53, 2006.
(PMC: 2430730) |
| 382. Physical principles of efficient excitation transfer in light
harvesting.
Melih Sener and Klaus Schulten.
In David L. Andrews, editor, Energy Harvesting Materials, pp.
1-26. World Scientific, Singapore, 2005.
|
| 388. Structural dynamics of the Lac repressor-DNA complex
revealed by a multiscale simulation.
Elizabeth Villa, Alexander Balaeff, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
102:6783-6788, 2005.
(PMC: 1100768) |
| 380. Molecular dynamics simulations of discoidal bilayers assembled from
truncated human lipoproteins.
Amy Y. Shih, Ilia G. Denisov, James C. Phillips, Stephen G. Sligar, and Klaus
Schulten.
Biophysical Journal, 88:548-556, 2005.
(PMC: 1305032) |
| 392. What makes an aquaporin a glycerol channel: A comparative study of
AqpZ and GlpF.
Yi Wang, Klaus Schulten, and Emad Tajkhorshid.
Structure, 13:1107-1118, 2005.
|
| 399. Biomolecular modeling using parallel supercomputers.
Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark
Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
In S. Aluru, editor, Handbook of computational molecular
biology, pp. 34.1-34.43. Taylor and Francis, 2005.
|
| 386. Approaches to developing biological H2-photoproducing organisms
and processes.
Maria L. Ghirardi, Paul W. King, Matthew C. Posewitz, Pin Ching Maness,
Alexander Fedorov, Kwiseon Kim, Jordi Cohen, Klaus Schulten, and Michael
Seibert.
Biochemical Society Transactions, 33:70-72, 2005.
|
| 394. Finding gas diffusion pathways in proteins: Application to O2
and H2 transport in CpI [FeFe]-hydrogenase and the role of packing
defects.
Jordi Cohen, Kwiseon Kim, Paul King, Michael Seibert, and Klaus Schulten.
Structure, 13:1321-1329, 2005.
|
| 402. Zooming in on ATP hydrolysis in F1.
Markus Dittrich and Klaus Schulten.
Journal of Bioenergetics and Biomembranes, 37:441-444, 2005.
(PMC: 1509602) |
| 398. Orientation discrimination of single stranded DNA inside the
α-hemolysin membrane channel.
Jerome Mathé, Aleksei Aksimentiev, David R. Nelson, Klaus Schulten, and
Amit Meller.
Proceedings of the National Academy of Sciences, USA,
102:12377-12382, 2005.
(PMC: 1194911) |
| 384. Kinetic theory and simulation of single-channel water transport.
Emad Tajkhorshid, Fangqiang Zhu, and Klaus Schulten.
In S. Yip, editor, Handbook of Materials Modeling, Vol. I:
Methods and Models, pp. 1797-1822. Springer, Netherlands, 2005.
|
| 396. Comparison of the light harvesting networks of plant and
cyanobacterial photosystem I.
Melih K. Sener, Craig Jolley, Adam Ben-Shem, Petra Fromme, Nathan Nelson,
Roberta Croce, and Klaus Schulten.
Biophysical Journal, 89:1630-1642, 2005.
(PMC: 1366667) |
| 403. Ion-nanotube terahertz oscillator.
Deyu Lu, Yan Li, Umberto Ravaioli, and Klaus Schulten.
Physical Review Letters, 95:246801, 2005.
(4 pages).
(PMC: 2492829) |
| 10004. Classical force field parameters for the heme prosthetic group of
cytochrome c.
F. Autenrieth, E. Tajkhorshid, J. Baudry, and Z. Luthey-Schulten.
Journal of Computational Chemistry, 25:1613-1622, 2004.
|
| 378. Collective diffusion model for water permeation through microscopic
channels.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Physical Review Letters, 93:224501, 2004.
(4 pages).
|
| 377. Finite-size effect and wall polarization in a carbon nanotube
channel.
Deyu Lu, Yan Li, Slava V. Rotkin, Umberto Ravaioli, and Klaus Schulten.
Nano Letters, 4:2383-2387, 2004.
|
| 376. Fluctuation-driven molecular transport through an asymmetric membrane
channel.
Ioan Kosztin and Klaus Schulten.
Physical Review Letters, 93:238102, 2004.
(4 pages).
|
| 375. Role of water in transient cytochrome c2 docking.
Felix Autenrieth, Emad Tajkhorshid, Klaus Schulten, and Zaida Luthey-Schulten.
Journal of Physical Chemistry B, 108:20376-20387, 2004.
|
| 374. Structural insights into how the MIDAS ion stabilizes integrin
binding to an RGD peptide under force.
David Craig, Mu Gao, Klaus Schulten, and Viola Vogel.
Structure, 12:2049-2058, 2004.
|
| 373. Molecular dynamics study of gating in the mechanosensitive channel of
small conductance MscS.
Marcos Sotomayor and Klaus Schulten.
Biophysical Journal, 87:3050-3065, 2004.
(PMC: 1304777) |
| 372. ATP hydrolysis in the βTP and
βDP catalytic sites of F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 87:2954-2967, 2004.
(PMC: 1304769) |
| 371. Microscopic kinetics of DNA translocation through synthetic
nanopores.
Aleksij Aksimentiev, Jiunn Benjamin Heng, Gregory Timp, and Klaus Schulten.
Biophysical Journal, 87:2086-2097, 2004.
(PMC: 1304610) |
| 370. Sizing DNA using a nanometer-diameter pore.
J. B. Heng, C. Ho, T. Kim, R. Timp, A. Aksimentiev, Y. V. Grinkova, S. Sligar,
K. Schulten, and G. Timp.
Biophysical Journal, 87:2905-2911, 2004.
(PMC: 1304707) |
| 369. Role of hydrogen-bond network in energy storage of
bacteriorhodopsin's light-driven proton pump revealed by ab initio
normal mode analysis.
Shigehiko Hayashi, Emad Tajkhorshid, Hideki Kandori, and Klaus Schulten.
Journal of the American Chemical Society, 126:10516-10517,
2004.
|
| 368. Computational studies of membrane channels.
Benoit Roux and Klaus Schulten.
Structure, 12:1343-1351, 2004.
|
| 367. A similarity measure for partially folded proteins: application to
unfolded and native-like conformational fluctuations.
Edgar Larios, Wei Y. Yang, Klaus Schulten, and Martin Gruebele.
Chemical Physics, 307:217-225, 2004.
|
| 366. Electronic structure and dielectric behavior of finite-length
single-walled carbon nanotubes.
Yan Li, Deyu Lu, Slava V. Rotkin, Klaus Schulten, and Umberto Ravaioli.
In Proceedings of the Fourth IEEE Conference on Nanotechnology,
pp. 273-275, Munich, Germany, 2004.
|
| 365. Complementarities and convergence of results in bacteriorhodopsin
trimer simulations.
Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 87:1394-1395, 2004.
(PMC: 1304478) |
| 364. Forced dissociation of the strand dimer interface between
C-cadherin ectodomains.
M. V. Bayas, K. Schulten, and D. Leckband.
Mechanics and Chemistry of Biosystems, 1:101-111, 2004.
|
| 363. Integrin activation in vivo and in silico.
Mu Gao and Klaus Schulten.
Structure, 12:2096-2098, 2004.
|
| 362. Multi-scale method for simulating protein-DNA complexes.
Elizabeth Villa, Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Multiscale Modeling and Simulation, 2:527-553, 2004.
|
| 361. Molecular dynamics simulations of micelle formation around dimeric
glycophorin A transmembrane helices.
Rosemary Braun, Donald M. Engelman, and Klaus Schulten.
Biophysical Journal, 87:754-763, 2004.
(PMC: 1304485) |
| 360. Multiple probes reveal a native-like intermediate during the
low-temperature refolding of ubiquitin.
E. Larios, J. S. Li, K. Schulten, H. Kihara, and M. Gruebele.
Journal of Molecular Biology, 340:115-125, 2004.
|
| 359. Excitation migration in trimeric cyanobacterial photosystem I.
Melih K. Sener, Sanghyun Park, Deyu Lu, Ana Damjanović, Thorsten Ritz,
Petra Fromme, and Klaus Schulten.
Journal of Chemical Physics, 120:11183-11195, 2004.
|
| 358. Extending the molecular modeling methodology to study insertion of
membrane nanopores.
Aleksij Aksimentiev and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
101:4337-4338, 2004.
(PMC: 384746) |
| 357. Lipid bilayer pressure profiles and mechanosensitive channel gating.
Justin Gullingsrud and Klaus Schulten.
Biophysical Journal, 86:3496-3509, 2004.
(PMC: 1304254) |
| 356. Calculating potentials of mean force from steered molecular dynamics
simulations.
Sanghyun Park and Klaus Schulten.
Journal of Chemical Physics, 120:5946-5961, 2004.
|
| 355. The mechanism of proton exclusion in aquaporin channels.
Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, and Gregory A. Voth.
PROTEINS: Structure, Function, and Bioinformatics, 55:223-228,
2004.
|
| 354. Mechanism of anionic conduction across CLC.
Jordi Cohen and Klaus Schulten.
Biophysical Journal, 86:836-845, 2004.
(PMC: 1303931) |
| 353. Modeling DNA loops using continuum and statistical mechanics.
Alexander Balaeff, Christophe R. Koudella, L. Mahadevan, and Klaus Schulten.
Philosophical Transactions of the Royal Society of London A. (Mathematical, Physical and Engineering Sciences), 362:1355-1371, 2004.
|
| 352. Insights into the molecular mechanism of rotation in the Fo sector
of ATP synthase.
Aleksij Aksimentiev, Ilya A. Balabin, Robert H. Fillingame, and Klaus Schulten.
Biophysical Journal, 86:1332-1344, 2004.
(PMC: 1303972) |
| 351. Tuning the mechanical stability of fibronectin type III modules
through sequence variation.
David Craig, Mu Gao, Klaus Schulten, and Viola Vogel.
Structure, 12:21-30, 2004.
|
| 350. Theory and simulation of water permeation in aquaporin-1.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 86:50-57, 2004.
(PMC: 1303818) |
| 349. Structural basis for cooperative DNA binding by CAP and
Lac repressor.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Structure, 12:123-132, 2004.
|
| 10003. Molecular basis of proton blockage in aquaporins.
Nilmadhab Chakrabarti, Emad Tajkhorshid, Benoît Roux, and Régis
Pomès.
Structure, 12:65-74, 2004.
|
| |
| 348. Molecular biomimetics: nanotechnology through biology.
Mehmet Sarikaya, Candan Tamerler, Alex K. -Y. Jen, Klaus Schulten, and
François Baneyx.
Nature Materials, 2:577-585, 2003.
|
| 347. Structure and functional significance of mechanically unfolded
fibronectin type III1 intermediates.
Mu Gao, David Craig, Olivier Lequin, Iain D. Campbell, Viola Vogel, and Klaus
Schulten.
Proceedings of the National Academy of Sciences, USA,
100:14784-14789, 2003.
(PMC: 299803) |
| 346. On the mechanism of ATP hydrolysis in F1-ATPase.
Markus Dittrich, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 85:2253-2266, 2003.
(PMC: 1303451) |
| 345. Glycerol conductance and physical asymmetry of the Escherichia
coli glycerol facilitator GlpF.
Deyu Lu, Paul Grayson, and Klaus Schulten.
Biophysical Journal, 85:2977-2987, 2003.
(PMC: 1303576) |
| 344. Electrostatic tuning of permeation and selectivity in aquaporin water
channels.
Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:2884-2899, 2003.
(PMC: 1303569) |
| 343. Gating of MscL studied by steered molecular dynamics.
Justin Gullingsrud and Klaus Schulten.
Biophysical Journal, 85:2087-2099, 2003.
(PMC: 1303438) |
| 342. Free energy calculation from steered molecular dynamics simulations
using Jarzynski's equality.
Sanghyun Park, Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten.
Journal of Chemical Physics, 119:3559-3566, 2003.
|
| 341. Molecular dynamics simulation of bacteriorhodopsin's
photoisomerization using ab initio forces for the excited chromophore.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:1440-1449, 2003.
(PMC: 1303320) |
| 340. Large scale simulation of protein mechanics and function.
Emad Tajkhorshid, Aleksij Aksimentiev, Ilya Balabin, Mu Gao, Barry Isralewitz,
James C. Phillips, Fangqiang Zhu, and Klaus Schulten.
In Frederic M. Richards, David S. Eisenberg, and John Kuriyan,
editors, Advances in Protein Chemistry, volume 66, pp. 195-247.
Elsevier Academic Press, New York, 2003.
|
| 339. Reaction paths based on mean first-passage times.
Sanghyun Park, Melih K. Sener, Deyu Lu, and Klaus Schulten.
Journal of Chemical Physics, 119:1313-1319, 2003.
|
| 338. Water and proton conduction through carbon nanotubes as models for
biological channels.
Fangqiang Zhu and Klaus Schulten.
Biophysical Journal, 85:236-244, 2003.
(PMC: 1303080) |
| 337. Mechanisms of selectivity in channels and enzymes studied with
interactive molecular dynamics.
Paul Grayson, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 85:36-48, 2003.
(PMC: 1303063) |
| 336. Forced detachment of the CD2-CD58 complex.
M. V. Bayas, Klaus Schulten, and D. Leckband.
Biophysical Journal, 84:2223-2233, 2003.
(PMC: 1302789) |
| 335. Identifying unfolding intermediates of FN-III10 by steered
molecular dynamics.
Mu Gao, David Craig, Viola Vogel, and Klaus Schulten.
Journal of Molecular Biology, 323:939-950, 2002.
|
| 334. Unfolding of titin domains studied by molecular dynamics simulations.
Mu Gao, Hui Lu, and Klaus Schulten.
Journal of Muscle Research and Cell Motility, 23:513-521,
2002.
|
| 333. Molecular dynamics investigation of primary photoinduced events in
the activation of rhodopsin.
Jan Saam, Emad Tajkhorshid, Shigehiko Hayashi, and Klaus Schulten.
Biophysical Journal, 83:3097-3112, 2002.
(PMC: 1302389) |
| 332. Steered molecular dynamics studies of titin I1 domain unfolding.
Mu Gao, Matthias Wilmanns, and Klaus Schulten.
Biophysical Journal, 83:3435-3445, 2002.
(PMC: 1302418) |
| 331. Robustness and optimality of light harvesting in cyanobacterial
photosystem I.
Melih K. Sener, Deyu Lu, Thorsten Ritz, Sanghyun Park, Petra Fromme, and
Klaus Schulten.
Journal of Physical Chemistry B, 106:7948-7960, 2002.
|
| 330. Genetically engineered gold-binding polypeptides: Structure
prediction and molecular dynamics.
Rosemary Braun, Mehmet Sarikaya, and Klaus Schulten.
Journal of Biomaterials Science, 13:747-758, 2002.
|
| 329. Control of the selectivity of the aquaporin water channel family by
global orientational tuning.
Emad Tajkhorshid, Peter Nollert, Morten O. Jensen, Larry J. W. Miercke,
Joseph O'Connell, Robert M. Stroud, and Klaus Schulten.
Science, 296:525-530, 2002.
|
| 328. Energetics of glycerol conduction through aquaglyceroporin GlpF.
Morten O. Jensen, Sanghyun Park, Emad Tajkhorshid, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
99:6731-6736, 2002.
(PMC: 124471) |
| 327. Pressure-induced water transport in membrane channels studied by
molecular dynamics.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 83:154-160, 2002.
(PMC: 1302135) |
| 326. What causes hyperfluorescence: folding intermediates or
conformationally flexible native states?
John Ervin, Edgar Larios, Szabolcs Osvath, Klaus Schulten, and Martin Gruebele.
Biophysical Journal, 83:473-483, 2002.
|
| 325. Structural changes during the formation of early intermediates in the
bacteriorhodopsin photocycle.
Shigehiko Hayashi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 83:1281-1297, 2002.
(PMC: 1302228) |
| 324. High pressure gel mobility shift analysis and molecular dynamics:
Investigating specific protein-nucleic acid recognition.
Thomas W. Lynch, Mark A. McLean, Dorina Kosztin, Klaus Schulten, and Stephen G.
Sligar.
In R. Hayashi, editor, Trends in High Pressure Bioscience and
Biotechnology, pp. 87-94. Elsevier, 2002.
|
| 323. Mechanical force generation by G-proteins.
Ioan Kosztin, Robijn Bruinsma, Paul O'Lague, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
99:3575-3580, 2002.
(PMC: 122565) |
| 322. Quasicontinuum representations of atomic-scale mechanics: From
proteins to dislocations.
Rob Phillips, Markus Dittrich, and Klaus Schulten.
Annual Review of Materials Research, 32:219-233, 2002.
|
| 321. The role of intersection topography in bond selectivity of
cis-trans photoisomerization.
Michal Ben-Nun, Ferenc Molnar, Klaus Schulten, and Todd J. Martinez.
Proceedings of the National Academy of Sciences, USA,
99:1769-1773, 2002.
(PMC: 122268) |
| 320. Excitons in a photosynthetic light-harvesting system: A combined
molecular dynamics, quantum chemistry and polaron model study.
Ana Damjanović, Ioan Kosztin, Ulrich Kleinekathoefer, and Klaus Schulten.
Physical Review E, 65:031919, 2002.
(24 pages).
|
| 319. A structural model for force regulated integrin binding to
fibronectin's RGD-synergy site.
André Krammer, David Craig, Wendy E. Thomas, Klaus Schulten, and Viola
Vogel.
Matrix Biology, 21:139-147, 2002.
|
| 317. Photosynthetic apparatus of purple bacteria.
Xiche Hu, Thorsten Ritz, Ana Damjanović, Felix Autenrieth, and Klaus
Schulten.
Quarterly Reviews of Biophysics, 35:1-62, 2002.
|
| 316. The quantum physics of photosynthesis.
Thorsten Ritz, Ana Damjanović, and Klaus Schulten.
ChemPhysChem, 3:243-248, 2002.
|
| 315. A general random matrix approach to account for the effect of static
disorder on the spectral properties of light harvesting systems.
Melih Sener and Klaus Schulten.
Physical Review E, 65:031916, 2002.
(12 pages).
|
| 314. Dissecting the molecular origins of protein-nucleic acid recognition:
Hydrostatic pressure and molecular dynamics.
Thomas W. Lynch, Dorina Kosztin, Mark A. McLean, Klaus Schulten, and Stephen G.
Sligar.
Biophysical Journal, 82:93-98, 2002.
(PMC: 1302451) |
| 318. The mechanism of glycerol conduction in aquaglyceroporins.
Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Structure, 9:1083-1093, 2001.
|
| 313. Molecular dynamics study of aquaporin-1 water channel in a lipid
bilayer.
Fangqiang Zhu, Emad Tajkhorshid, and Klaus Schulten.
FEBS Letters, 504:212-218, 2001.
|
| 312. Structural determinants of spectral tuning in retinal proteins -
bacteriorhodopsin vs sensory rhodopsin II.
Shigehiko Hayashi, Emad Tajkhorshid, Eva Pebay-Peyroula, Antoine Royant,
Ehud M. Landau, Javier Navarro, and Klaus Schulten.
Journal of Physical Chemistry B, 105:10124-10131, 2001.
|
| 311. Kinetics of excitation migration and trapping in the photosynthetic
unit of purple bacteria.
Thorsten Ritz, Sanghyun Park, and Klaus Schulten.
Journal of Physical Chemistry B, 105:8259-8267, 2001.
|
| 310. Simulated refolding of stretched titin immunoglobulin domains.
Mu Gao, Hui Lu, and Klaus Schulten.
Biophysical Journal, 81:2268-2277, 2001.
(PMC: 1301698) |
| 309. Comparison of the early stages of forced unfolding of fibronectin
type III modules.
David Craig, André Krammer, Klaus Schulten, and Viola Vogel.
Proceedings of the National Academy of Sciences, USA,
98:5590-5595, 2001.
(PMC: 33257) |
| 308. Structural determinants of MscL gating studied by molecular
dynamics simulations.
Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten.
Biophysical Journal, 80:2074-2081, 2001.
(PMC: 1301400) |
| 307. Steered molecular dynamics and mechanical functions of proteins.
Barry Isralewitz, Mu Gao, and Klaus Schulten.
Current Opinion in Structural Biology, 11:224-230, 2001.
|
| 306. Physik der Photosynthese.
Thorsten Ritz and Klaus Schulten.
Physikalische Blaetter, 57:49-53, 2001.
|
| 305. Phylogenetic analysis of metabolic pathways.
Christian Forst and Klaus Schulten.
Journal of Molecular Evolution, 52:471-489, 2001.
|
| 304. A system for interactive molecular dynamics simulation.
John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten.
In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM
Symposium on Interactive 3D Graphics, pp. 191-194, New York, 2001. ACM
SIGGRAPH.
|
| 303. Steered molecular dynamics investigations of protein function.
Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus
Schulten.
Journal of Molecular Graphics and Modeling, 19:13-25, 2001.
Also in Protein Flexibility and Folding, L. A. Kuhn and M. F.
Thorpe, editors, Biological Modeling Series (Elsevier).
|
| 302. Molecular dynamics study of bacteriorhodopsin and the purple
membrane.
Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus
Schulten.
Journal of Physical Chemistry B, 105:905-918, 2001.
|
| 301. Efficient light harvesting through carotenoids.
Thorsten Ritz, Ana Damjanović, Klaus Schulten, Jian-Ping Zhang, and
Yasushi Koyama.
Photosynthesis Research, 66:125-144, 2000.
|
| 300. The key event in force-induced unfolding of titin's immunoglobulin
domains.
Hui Lu and Klaus Schulten.
Biophysical Journal, 79:51-65, 2000.
(PMC: 1300915) |
| 299. To students contemplating research in biomolecular modelling.
Klaus Schulten.
Journal of Molecular Graphics and Modeling, 18:218-220, 2000.
|
| 298. Calculations suggest a pathway for the transverse diffusion of a
hydrophobic peptide across a lipid bilayer.
Amit Kessel, Klaus Schulten, and Nir Ben-Tal.
Biophysical Journal, 79:2322-2330, 2000.
(PMC: 1301120) |
| 297. Electron transfer: Exploiting thermal motion.
Klaus Schulten.
Science, 290:61-62, 2000.
|
| 296. Excitation transfer in the peridinin-chlorophyll-protein of
Amphidinium carterae.
Ana Damjanović, Thorsten Ritz, and Klaus Schulten.
Biophysical Journal, 79:1695-1705, 2000.
(PMC: 1301064) |
| 295. Simulated unbinding and binding of fatty acid substrates in the
cyclooxygenase site of prostaglandin H2 synthase-1.
Ferenc Molnar, Lawrence S. Norris, and Klaus Schulten.
Progress in Reaction Kinetics and Mechanism, 25:263-298, 2000.
|
| 294. Speech/gesture interface to a visual-computing environment.
Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo,
Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten.
IEEE Computer Graphics and Applications, 20:29-37, 2000.
|
| 293. Characterization of a conical intersection between the ground and
first excited state for a retinal analog.
Ferenc Molnar, Michal Ben-Nun, Todd J. Martínez, and Klaus Schulten.
Journal of Molecular Structure (THEOCHEM), WATOC special
issue, 506:169-178, 2000.
|
| 292. The fast multipole algorithm.
John Board and Klaus Schulten.
IEEE Computational Science & Engineering, 2:56-59, 2000.
|
| 288. Excitation energy trapping by the reaction center of
Rhodobacter sphaeroides.
Ana Damjanović, Thorsten Ritz, and Klaus Schulten.
Int. J. Quantum Chem., 77:139-151, 2000.
|
| 289. Evolution of metabolisms: A new method for the comparison of
metabolic pathways using genomics information.
Christian Forst and Klaus Schulten.
Journal of Computational Biology, 6:343-360, 1999.
|
| 287. A model for photoreceptor-based magnetoreception in birds.
Thorsten Ritz, Salih Adem, and Klaus Schulten.
Biophysical Journal, 78:707-718, 2000.
(PMC: 1300674) |
| 285. Molecular dynamics study of the nature and origin of retinal's
twisted structure in bacteriorhodopsin.
Emad Tajkhorshid, Jerome Baudry, Klaus Schulten, and Sandor Suhai.
Biophysical Journal, 78:683-693, 2000.
(PMC: 1300671) |
| 284. Computer modeling of force-induced titin domain unfolding.
Hui Lu, André Krammer, Barry Isralewitz, Viola Vogel, and Klaus Schulten.
In Jerry Pollack and Henk Granzier, editors, Elastic Filaments
of the Cell, chapter 1, pp. 143-162. Kluwer Academic/Plenum Publishers, New
York, NY, 2000.
|
| 291. Group report: How does complexity lead to an apparently simple
function?
K. Moffat, J.-P. Changeux, D. M. Crothers, H. Grubmueller, G. U. Nienhaus,
M. U. Palma, F. G. Parak, K. Schulten, and A. Warshel.
In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors,
Simplicity and Complexity in Proteins and Nucleic Acids, pp. 255-280,
Berlin, 1999. Dahlem University Press.
|
| 290. Elastic rod model of a DNA loop in the lac operon.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Physical Review Letters, 83:4900-4903, 1999.
|
| 286. Mechanical unfolding intermediates in titin modules.
Piotr E. Marszalek, Hui Lu, Hongbin Li, Mariano Carrion-Vazquez, Andres F.
Oberhauser, Klaus Schulten, and Julio M. Fernandez.
Nature, 402:100-103, 1999.
|
| 283. Steered molecular dynamics simulation of the Rieske subunit motion
in the cytochrome bc1 complex.
Sergei Izrailev, Antony R. Crofts, Edward A. Berry, and Klaus Schulten.
Biophysical Journal, 77:1753-1768, 1999.
|
| 282. Probing the role of structural water in a duplex
oligodeoxyribonucleotide containing a water-mimicking base analogue.
Dorina Kosztin, Richard Gumport, and Klaus Schulten.
Nucleic Acids Research, 27:3550-3556, 1999.
(PMC: 148600) |
| 281. Steered molecular dynamics simulation of conformational changes of
immunoglobulin domain I27 interpret atomic force microscopy observations.
Hui Lu and Klaus Schulten.
Chemical Physics, 247:141-153, 1999.
|
| 280. Evolution of metabolisms: A new method for the comparison of
metabolic pathways.
Christian V. Forst and Klaus Schulten.
In Sorin Istrail, Pavel Pevzner, and Michael Waterman, editors,
Proceedings of the Third Annual International Conference on Computational
Molecular Biology, pp. 174-180, Lyon, France, 1999. ACM Press, New York.
|
| 279. Steered molecular dynamics simulations of force-induced protein
domain unfolding.
Hui Lu and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 35:453-463, 1999.
|
| 278. Algorithmic challenges in computational molecular biophysics.
Tamar Schlick, Robert Skeel, Axel Brünger, Laxmikant Kalé, John A. Board
Jr., Jan Hermans, and Klaus Schulten.
Journal of Computational Physics, 151:9-48, 1999.
|
| 277. Forced unfolding of the fibronectin type III module reveals a
tensile molecular recognition switch.
André Krammer, Hui Lu, Barry Isralewitz, Klaus Schulten, and Viola Vogel.
Proceedings of the National Academy of Sciences, USA,
96:1351-1356, 1999.
(PMC: 15466) |
| 276. NAMD2: Greater scalability for parallel molecular dynamics.
Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila
Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan
Varadarajan, and Klaus Schulten.
Journal of Computational Physics, 151:283-312, 1999.
|
| 275. Reconstructing potentials of mean force through time series analysis
of steered molecular dynamics simulations.
Justin Gullingsrud, Rosemary Braun, and Klaus Schulten.
Journal of Computational Physics, 151:190-211, 1999.
|
| 274. Investigating a back door mechanism of actin phosphate release by
steered molecular dynamics.
Willy Wriggers and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 35:262-273, 1999.
|
| 272. BioCoRE: A collaboratory for structural biology.
Milind Bhandarkar, Gila Budescu, William Humphrey, Jesus A. Izaguirre, Sergei
Izrailev, Laxmikant V. Kalé, Dorina Kosztin, Ferenc Molnar, James C.
Phillips, and Klaus Schulten.
In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page,
editors, Proceedings of the SCS International Conference on Web-Based
Modeling and Simulation, pp. 242-251, San Francisco, California, 1999.
|
| 270. Unbinding of retinoic acid from its receptor studied by steered
molecular dynamics.
Dorina Kosztin, Sergei Izrailev, and Klaus Schulten.
Biophysical Journal, 76:188-197, 1999.
|
| 268. From simplicity to complexity and back: Function, architecture and
mechanism of light harvesting systems in photosynthetic bacteria.
Klaus Schulten.
In H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, editors,
Simplicity and Complexity in Proteins and Nucleic Acids, pp. 227-253,
Berlin, 1999. Dahlem University Press.
(pdf available from author upon request).
|
| 267. Expansion method for stationary states of quantum billiards.
David Kaufman, Ioan Kosztin, and Klaus Schulten.
American Journal of Physics, 67:133-141, 1999.
|
| 264. Energy transfer between carotenoids and bacteriochlorophylls in a
light harvesting protein.
Ana Damjanović, Thorsten Ritz, and Klaus Schulten.
Physical Review E, 59:3293-3311, 1999.
|
| 273. Self-organizing neural networks bridge the biomolecular resolution
gap.
Willy Wriggers, Ronald A. Milligan, Klaus Schulten, and J. Andrew McCammon.
Journal of Molecular Biology, 284:1247-1254, 1998.
|
| 271. Light-harvesting and photoprotection by carotenoids:
Structure-based calculations for photosynthetic antenna systems.
Thorsten Ritz, Ana Damjanović, and Klaus Schulten.
In G. Garab, editor, Photosynthesis: Mechanisms and Effects
(Proceedings of the XIth International Congress on Photosynthesis),
volume 1, pp. 487-490, Dordrecht, 1998. Kluwer Academic Publications.
|
| 269. Electronic excitations in aggregates of bacteriochlorophylls.
Marshall G. Cory, Michael C. Zerner, Xiche Hu, and Klaus Schulten.
Journal of Physical Chemistry B, 102:7640-7650, 1998.
|
| 266. Three electronic state model of the primary phototransformation of
bacteriorhodopsin.
W. Humphrey, H. Lu, I. Logunov, H. J. Werner, and K. Schulten.
Biophysical Journal, 75:1689-1699, 1998.
|
| 265. Unfolding of titin immunoglobulin domains by steered molecular
dynamics simulation.
Hui Lu, Barry Isralewitz, André Krammer, Viola Vogel, and Klaus Schulten.
Biophysical Journal, 75:662-671, 1998.
|
| 263. A model for the light-harvesting complex I (B875) of
Rhodobacter sphaeroides.
Xiche Hu and Klaus Schulten.
Biophysical Journal, 75:683-694, 1998.
|
| 262. Quantum dynamics of retinal's femtosecond photoisomerization in
bacteriorhodopsin.
Michal Ben-Nun, Ferenc Molnar, Hui Lu, James C. Phillips, Todd J.
Martínez, and Klaus Schulten.
In Faraday Discussions, No. 110, pp. 447-462. Faraday
Publications, 1998.
|
| 261. Structure and dynamics of calmodulin in solution.
Willy Wriggers, Ernest Mehler, Felicia Pitici, Harel Weinstein, and Klaus
Schulten.
Biophysical Journal, 74:1622-1639, 1998.
|
| 260. The use of solid physical models for the study of macromolecular
assembly.
Michael Bailey, Klaus Schulten, and John E. Johnson.
Current Opinion in Structural Biology, 8:202-208, 1998.
|
| 259. Architecture and function of the light harvesting apparatus of purple
bacteria.
Xiche Hu, Ana Damjanović, Thorsten Ritz, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
95:5935-5941, 1998.
(PMC: 34498) |
| 258. Nucleotide-dependent movements of the kinesin motor domain predicted
by simulated annealing.
Willy Wriggers and Klaus Schulten.
Biophysical Journal, 75:646-661, 1998.
|
| 256. Avoiding algorithmic obfuscation in a message-driven parallel MD
code.
James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal
Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A. Mark, S. Reich, and
R. D. Skeel, editors, Computational Molecular Dynamics: Challenges,
Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
Engineering, pp. 472-482. Springer-Verlag, 1998.
|
| 255. Steered molecular dynamics.
Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu,
Ferenc Molnar, Willy Wriggers, and Klaus Schulten.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and
R. D. Skeel, editors, Computational molecular dynamics: challenges,
methods, ideas, volume 4 of Lecture notes in computational science and
engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
|
| 254. Excitons and excitation transfer in the photosynthetic unit of purple
bacteria.
Thorsten Ritz, Xiche Hu, Ana Damjanović, and Klaus Schulten.
Journal of Luminescence, 76-77:310-321, 1998.
|
| 253. Structure prediction of a complex between the chromosomal protein
HMG-D and DNA.
Alexander Balaeff, Mair E. A. Churchill, and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 30:113-135, 1998.
|
| 252. Oxygen and proton pathways in cytochrome c oxidase.
Ivo Hofacker and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 30:100-107, 1998.
|
| 257. A three-dimensional model of the morphogenesis of the rhesus lateral
geniculate nucleus.
Svilen Tzonev, Joseph Malpeli, and Klaus Schulten.
Beckman Institute Technical Report, University of Illinois, 1998.
|
| 251. Extraction of lipids from phospholipid membranes by steered molecular
dynamics.
Sergey Stepaniants, Sergei Izrailev, and Klaus Schulten.
Journal of Molecular Modeling, 3:473-475, 1997.
|
| 250. Binding pathway of retinal to bacterio-opsin: A prediction by
molecular dynamics simulations.
Barry Isralewitz, Sergei Izrailev, and Klaus Schulten.
Biophysical Journal, 73:2972-2979, 1997.
(PMC: 1181203) |
| 249. Predicting the structure of apolipoprotein A-I in reconstituted
high density lipoprotein disks.
James C. Phillips, Willy Wriggers, Zhigang Li, Ana Jonas, and Klaus Schulten.
Biophysical Journal, 73:2337-2346, 1997.
(PMC: 1181137) |
| 248. How nature harvests sunlight.
Xiche Hu and Klaus Schulten.
Physics Today, 50:28-34, 1997.
|
| 247. A visual computing environment for very large scale biomolecular
modeling.
Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus
Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and
S. Chu.
In Proceedings of the 1997 IEEE International Conference on
Application-specific Systems, Architectures and Processors (ASAP), pp.
3-12. IEEE Computer Society Press, 1997.
|
| 246. Learning the perceptual control manifold for sensor-based robot path
planning.
Michael Zeller, Rajeev Sharma, and Klaus Schulten.
In Proceedings of the 1997 IEEE International Symposium on
Computational Intelligence in Robotics and Automation (CIRA'97), pp.
48-53. IEEE Computer Society Press, 1997.
|
| 245. Stability and dynamics of G-actin: Back door water diffusion and
behavior of a subdomain 3/4 loop.
Willy Wriggers and Klaus Schulten.
Biophysical Journal, 73:624-639, 1997.
(PMC: 1180962) |
| 244. Reconstructing potential energy functions from simulated
force-induced unbinding processes.
Manel Balsera, Sergey Stepaniants, Sergei Izrailev, Yoshitsugu Oono, and Klaus
Schulten.
Biophysical Journal, 73:1281-1287, 1997.
|
| 243. Binding of the estrogen receptor to DNA: The role of waters.
Dorina Kosztin, Thomas C. Bishop, and Klaus Schulten.
Biophysical Journal, 73:557-570, 1997.
(PMC: 1180957) |
| 242. Difficulties with multiple time stepping and the fast multipole
algorithm in molecular dynamics.
Thomas C. Bishop, Robert D. Skeel, and Klaus Schulten.
Journal of Computational Chemistry, 18:1785-1791, 1997.
|
| 241. Protein domain movements: Detection of rigid domains and
visualization of hinges in comparisons of atomic coordinates.
Willy Wriggers and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 29:1-14, 1997.
|
| 240. Pigment organization and transfer of electronic excitation in the
purple bacteria.
Xiche Hu, Thorsten Ritz, Ana Damjanović, and Klaus Schulten.
Journal of Physical Chemistry B, 101:3854-3871, 1997.
|
| 239. Boundary integral method for stationary states of two-dimensional
quantum systems.
Ioan Kosztin and Klaus Schulten.
Int. J. of Modern Phys. C, 8:293-325, 1997.
|
| 238. Vision-based robot motion planning using a topology representing
neural network.
Michael Zeller, Rajeev Sharma, and Klaus Schulten.
In Jens Kalkkuhl, Ken Hunt, Rafal Zbikowski, and Andrzej Dzielinski,
editors, Applications of Neural Adaptive Control Technology, volume 17
of World Scientific Series in Robotics and Intelligent Systems, pp.
181-204. World Scientific Publishing, 1997.
|
| 237. How hormone receptor-DNA binding affects nucleosomal DNA: The
role of symmetry.
Tom Connor Bishop, Dorina Kosztin, and Klaus Schulten.
Biophysical Journal, 72:2056-2067, 1997.
(PMC: 1184400) |
| 236. Molecular dynamics study of unbinding of the avidin-biotin complex.
Sergei Izrailev, Sergey Stepaniants, Manel Balsera, Yoshi Oono, and Klaus
Schulten.
Biophysical Journal, 72:1568-1581, 1997.
(PMC: 1184352) |
| 235. Motion planning of a pneumatic robot using a neural network.
Michael Zeller, Rajeev Sharma, and Klaus Schulten.
IEEE Control Systems Magazine, 17:89-98, 1997.
|
| 234. Photoproducts of bacteriorhodopsin mutants: A molecular dynamics
study.
William Humphrey, Ernst Bamberg, and Klaus Schulten.
Biophysical Journal, 72:1347-1356, 1997.
(PMC: 1184517) |
| 233. Theory of heterogeneous relaxation in compartmentalized tissues.
Daniel Barsky, Benno Pütz, and Klaus Schulten.
Magnetic Resonance in Medicine, 37:666-675, 1997.
|
| 232. Using TCL for molecular visualization and analysis.
Andrew Dalke and Klaus Schulten.
In Proceedings of the Pacific Symposium on Biocomputing
'97, volume 2, pp. 85-96, 1997.
|
| 221. Probing protein motion through temperature echoes.
Klaus Schulten, Hui Lu, and Linsen Bai.
In Henrik Flyvbjerg, John Hertz, Mogens H. Jensen, Ole G. Mouritsen,
and Kim Sneppen, editors, Physics of Biological Systems: From Molecules
to Species, Lecture Notes in Physics, pp. 117-152. Springer, 1997.
|
| 231. Analysis and control of a rubbertuator arm.
P. van der Smagt, F. Grön, and K. Schulten.
Biological Cybernetics, 75:433-440, 1996.
|
| 230. Vision-based motion planning of a pneumatic robot using a topology
representing neural network.
Michael Zeller, Rajeev Sharma, and Klaus Schulten.
In Proceedings of 1996 IEEE Int. Symposium on Intelligent
Control, pp. 7-12, 1996.
|
| 229. Topology representing network for sensor-based robot motion planning.
Michael Zeller, Rajeev Sharma, and Klaus Schulten.
In Proceedings of the 1996 World Congress on Neural Networks,
pp. 100-103. INNS Press, 1996.
|
| 228. Quantum chemistry - molecular dynamics study of the dark adaptation
process in bacteriorhodopsin.
Ilya Logunov and Klaus Schulten.
Journal of the American Chemical Society, 118:9727-9735, 1996.
|
| 227. Speech/gesture interface to a visual computing environment for
molecular biologists.
R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips,
M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu.
In Proceedings of 13th ICPR 96, volume 3, pp. 964-968, 1996.
|
| 226. NAMD - A parallel, object-oriented molecular dynamics program.
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert D. Skeel, and Klaus Schulten.
International Journal of Supercomputer Applications and High
Performance Computing, 10:251-268, 1996.
|
| 225. The crystal structure of the light harvesting complex II
(B800-850) from Rhodospirillum molischianum.
Juergen Koepke, Xiche Hu, Cornelia Muenke, Klaus Schulten, and Hartmut Michel.
Structure, 4:581-597, 1996.
|
| 224. Protein response to external electric fields: Relaxation, hysteresis,
and echo.
Dong Xu, James Christopher Phillips, and Klaus Schulten.
Journal of Physical Chemistry, 100:12108-12121, 1996.
|
| 223. Molecular dynamics study of the activation of phospholipase A2
on a membrane surface.
Feng Zhou and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 25:12-27, 1996.
|
| 222. VMD - Visual Molecular Dynamics.
William Humphrey, Andrew Dalke, and Klaus Schulten.
Journal of Molecular Graphics, 14:33-38, 1996.
|
| 220. Principal component analysis and long time protein dynamics.
Manel A. Balsera, Willy Wriggers, Yoshitsugu Oono, and Klaus Schulten.
Journal of Physical Chemistry, 100:2567-2572, 1996.
|
| 218. Molecular dynamics study of early picosecond events in the
bacteriorhodopsin photocycle: Dielectric response, vibrational cooling and
the J, K intermediates.
Dong Xu, Charles Martin, and Klaus Schulten.
Biophysical Journal, 70:453-460, 1996.
(PMC: 1224943) |
| 217. Topology representing maps and brain function.
Klaus Schulten and Michael Zeller.
In Nova Acta Leopoldina NF, volume 72, pp. 133-157.
Jahresversammlungsband, 1996.
|
| 209. Molecular dynamics study of glucocorticoid receptor-DNA binding.
Thomas C. Bishop and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 24:115-133, 1996.
|
| 203. Prediction of the structure of an integral membrane protein-the
light-harvesting complex II of Rhodospirillum molischianum.
Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jürgen Koepke, and Hartmut
Michel.
In K.M. Merz and B. Roux, editors, Biological Membranes: A
Molecular Perspective from Computation and Experiment, pp. 503-533.
Birkhäuser, Cambridge, MA, 1996.
|
| 202. Knowledge-based structure prediction of the light-harvesting complex
II of Rhodospirillum molischianum.
Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jürgen Koepke, and Hartmut
Michel.
In P. M. Pardalos, D. Shalloway, and G. Xue, editors, Global
Minimization of Nonconvex Energy Functions: Molecular Conformation and
Protein Folding, pp. 97-122. American Mathematical Society, Providence,
R.I., 1996.
|
| 201. Introduction to the diffusion Monte Carlo method.
Ioan Kosztin, Byron Faber, and Klaus Schulten.
American Journal of Physics, 64:633-644, 1996.
|
| 183. Topology representing network in robotics.
Kakali Sarkar and Klaus Schulten.
In J. Leo van Hemmen, Eytan Domany, and Klaus Schulten, editors,
Models of Neural Networks, volume 3 of Physics of Neural Networks, pp.
281-302. Springer-Verlag, New York, 1996.
|
| 219. A numerical study of learning curves in stochastic multi-layer
feed-forward networks.
K.-R. Müller, N. Murata, M. Finke, K. Schulten, and S. Amari.
Neural Computation, 8:1085-1106, 1995.
|
| 216. Molecular dynamics study of the M412 intermediate of
bacteriorhodopsin.
Dong Xu, Mordechai Sheves, and Klaus Schulten.
Biophysical Journal, 69:2745-2760, 1995.
(PMC: 1236512) |
| 215. A perturbation treatment of oscillating magnetic fields in the
radical pair mechanism using the Liouville equation.
J. M. Canfield, R. L. Belford, P. G. Debrunner, and K. Schulten.
Chemical Physics, 195:59-69, 1995.
|
| 214. Curve crossing in a protein: Coupling of the elementary quantum
process to motions of the protein.
Klaus Schulten.
In D. Bicout and M. J. Field, editors, Proceedings of the Ecole
de Physique des Houches, pp. 85-118, Paris, 1995. Les Editions de Physique,
Springer.
|
| 213. Quantum chemistry of in situ retinal: Study of the spectral
properties and dark adaptation of bacteriorhodopsin.
Ilya Logunov and Klaus Schulten.
In D. Bicout and M. J. Field, editors, Proceedings of the Ecole
de Physique des Houches, pp. 235-256, Paris, 1995. Les Editions de
Physique, Springer.
|
| 212. Biological visuo-motor control of a pneumatic robot arm.
Michael Zeller, K. R. Wallace, and Klaus Schulten.
In Dagli et al., editors, Intelligent Engineering Systems
Through Artificial Neural Networks, volume 5, pp. 645-650, New York, 1995.
American Society of Mechanical Engineers.
|
| 211. Molecular dynamics study of the early intermediates in the
bacteriorhodopsin photocycle.
William Humphrey, Dong Xu, Mordechai Sheves, and Klaus Schulten.
Journal of Physical Chemistry, 99:14549-14560, 1995.
|
| 210. Molecular dynamics studies of bacteriorhodopsin's photocycles.
Klaus Schulten, William Humphrey, Ilya Logunov, Mordechai Sheves, and Dong Xu.
Israel Journal of Chemistry, 35:447-464, 1995.
|
| 208. Predicting the structure of the light-harvesting complex II of
Rhodospirillum molischianum.
Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jürgen Koepke, and Hartmut
Michel.
Protein Science, 4:1670-1682, 1995.
|
| 207. MDScope - A visual computing environment for structural biology.
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin.
In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors,
Computational Mechanics 95, volume 1, pp. 476-481, 1995.
|
| 206. Diffusive hysteresis at high and low driving frequencies.
James Phillips and Klaus Schulten.
Physical Review E, 52:2473-2477, 1995.
|
| 205. A perturbation theory treatment of oscillating magnetic fields in the
radical pair mechanism - Erratum.
Jeff M. Canfield, R. Linn Belford, Peter G. Debrunner, and Klaus Schulten.
Chemical Physics, 191:347-347, 1995.
|
| 204. Large scale simulations for learning curves.
K.-R. Müller, M. Finke, N. Murata, K. Schulten, and S. Amari.
In Jong-Hoon Oh, Chulan Kwon, and Sungzoon Cho, editors,
Progress in neural Processing Vol. 1 / Neural Networks: The Statistical
Mechanics Perspective, pp. 73-84. World Scientific, Singapore, 1995.
|
| 200. Velocity reassignment echoes in proteins.
Dong Xu and Klaus Schulten.
Journal of Chemical Physics, 103:3124-3139, 1995.
|
| 199. Temperature quench echoes in proteins.
Dong Xu, Klaus Schulten, Oren M. Becker, and Martin Karplus.
Journal of Chemical Physics, 103:3112-3123, 1995.
|
| 198. A molecular dynamics simulation of immobilized artificial membranes.
Qing Sheng, Klaus Schulten, and Charles Pidgeon.
Journal of Physical Chemistry, 99:11018-11027, 1995.
|
| 197. Modeling AFM tip dynamics through diffusion in time-periodic
potentials.
James Phillips and Klaus Schulten.
Beckman Institute Technical Report TB-95-03, University of Illinois,
1995.
|
| 195. MDScope - A visual computing environment for structural biology.
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin.
Computational Physics Communications, 91:111-134, 1995.
|
| 194. Noise-induced neuronal oscillations.
Christian Kurrer and Klaus Schulten.
Physical Review E, 51:6213-6218, 1995.
|
| 193. Molecular dynamics study of a membrane-water interface.
Feng Zhou and Klaus Schulten.
Journal of Physical Chemistry, 99:2194-2208, 1995.
|
| 192. Molecular dynamics study of the 13-cis form (bR548) of
bacteriorhodopsin and its photocycle.
Ilya Logunov, William Humphrey, Klaus Schulten, and Mordechai Sheves.
Biophysical Journal, 68:1270-1282, 1995.
(PMC: 1282023) |
| 191. Models of orientation and ocular dominance columns in the visual
cortex: A critical comparison.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
Neural Computation, 7:425-468, 1995.
|
| 190. Morphogenesis of the lateral geniculate nucleus: How singularities
affect global structure.
Svilen Tzonev, Joseph Malpeli, and Klaus Schulten.
In G. Tesauro, D. Touretzky, and T. Leen, editors, Advances in
Neural Information Processing Systems 7, pp. 133-140, Cambridge, Mass and
London, England, 1995. MIT Press.
|
| 189. A critical comparison of models for orientation and ocular dominance
columns in the striate cortex.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
In G. Tesauro, D. Touretzky, and T. Leen, editors, Advances in
Neural Information Processing Systems 7, pp. 93-100. MIT Press, Cambridge,
Mass and London, England, 1995.
|
| 188. Molecular dynamics on parallel computers: Applications for
theoretical biophysics.
Thomas C. Bishop, Helmut Heller, and Klaus Schulten.
In Rajiv K. Kalia and Priya Vashishta, editors, Toward Teraflop
Computing and New Grand Challenge Applications, pp. 129-138. Nova Science
Publishers, Inc., New York, 1995.
|
| 196. Modeling biomolecules: Larger scales, longer durations.
John A. Board, Jr., Laxmikant V. Kalé, Klaus Schulten, Robert D. Skeel, and
Tamar Schlick.
IEEE Computational Science & Engineering, Winter:19-30,
1994.
|
| 187. A perturbation theory treatment of oscillating magnetic fields in the
radical pair mechanism.
Jeff M. Canfield, R. Linn Belford, Peter G. Debrunner, and Klaus Schulten.
Chemical Physics, 182:1-18, 1994.
|
| 186. Molecular dynamics study of a sequence specific protein-DNA
interaction.
Thomas C. Bishop and Klaus Schulten.
In G. Wipff, editor, Computational Approaches in Supramolecular
Chemistry, pp. 419-439. Kluwer Academic Publishers, Boston, 1994.
|
| 185. Molecular dynamics study of bacteriorhodopsin and artificial
pigments.
William Humphrey, Ilya Logunov, Klaus Schulten, and Mordechai Sheves.
Biochemistry, 33:3668-3678, 1994.
|
| 184. Mechanisms of liposomal contrast agents in magnetic resonance
imaging.
Benno Pütz, Daniel Barsky, and Klaus Schulten.
Journal of Liposome Research, 4:771-808, 1994.
|
| 178. Topology representing networks.
Thomas Martinetz and Klaus Schulten.
Neural Networks, 7:507-522, 1994.
|
| 175. Neural network control of a pneumatic robot arm.
Ted Hesselroth, Kakali Sarkar, P. Patrick van der Smagt, and Klaus Schulten.
IEEE Transactions on Systems, Man, and Cybernetics,
24:28-37, 1994.
|
| 174. Performance analysis of a parallel molecular dynamics program.
Amitabh B. Sinha, Klaus Schulten, and Helmut Heller.
Computational Physics Communications, 78:265-278, 1994.
|
| 166. Coupling of protein motion to electron transfer in a photosynthetic
reaction center: Investigating the low temperature behaviour in the framework
of the spin-boson model.
Dong Xu and Klaus Schulten.
Chemical Physics, 182:91-117, 1994.
|
| 182. A neural network with Hebbian-like adaptation rules learning
visuomotor coordination of a PUMA robot.
Thomas Martinetz and Klaus Schulten.
In Proceedings of the IEEE International Conference on Neural
Networks (ICNN-93), San Francisco, pp. 820-825, 1993.
|
| 181. Control of pneumatic robot arm dynamics by a neural network.
Patrick van der Smagt and Klaus Schulten.
In Proceedings of the World Congress on Neural Networks,
Portland, OR, July 11-15, volume 3, pp. 180-183, 1993.
|
| 180. A comparison of models of visual cortical map formation.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
In Frank H. Eeckman and James M. Bower, editors, Computation and
Neural Systems, chapter 60, pp. 395-402. Kluwer Academic Publishers, 1993.
|
| 179. Molecular dynamics simulation of a bilayer of 200 lipids in the gel
and in the liquid crystal-phases.
Helmut Heller, Michael Schaefer, and Klaus Schulten.
Journal of Physical Chemistry, 97:8343-8360, 1993.
|
| 177. Dependence of percolation thresholds on lattice connectivity.
Christian Kurrer and Klaus Schulten.
Physical Review E, 48:614-617, 1993.
|
| 169. Molecular dynamics study of the proton pump cycle of
bacteriorhodopsin.
Feng Zhou, Andreas Windemuth, and Klaus Schulten.
Biochemistry, 32:2291-2306, 1993.
|
| 168. Implementation of self-organizing neural networks for visuo-motor
control of an industrial robot.
Jörg A. Walter and Klaus Schulten.
IEEE Transactions on Neural Networks, 4:86-95, 1993.
|
| 173. Accelerated molecular dynamics simulation with the parallel fast
multipole algorithm.
John A. Board, Jr., J. W. Causey, James F. Leathrum, Jr., Andreas Windemuth,
and Klaus Schulten.
Chemical Physics Letters, 198:89-94, 1992.
|
| 176. Multi-mode coupling of protein motion to electron transfer in the
photosynthetic reaction center: Spin-boson theory based on a classical
molecular dynamics simulation.
Dong Xu and Klaus Schulten.
In J. Breton and A. Vermeglio, editors, The Photosynthetic
Bacterial Reaction Center: II. Structure, Spectroscopy and Dynamics,
NATO Science Series A: Life Sciences, pp. 301-312. Plenum Press, New
York, 1992.
|
| 172. Diffusional edge enhancement observed by NMR in thin glass
capillaries.
Daniel Barsky, Benno Pütz, Klaus Schulten, J. Schoeniger, E. W. Hsu, and
S. Blackband.
Chemical Physics Letters, 200:88-96, 1992.
|
| 171. Parallel distributed computing for molecular dynamics: Simulation of
large heterogeneous systems on a systolic ring of transputers.
Helmut Heller and Klaus Schulten.
Chemical Design Automation News, 7:11-22, 1992.
|
| 170. A comparison between a neural network model for the formation of
brain maps and experimental data.
Klaus Obermayer, Klaus Schulten, and Gary G. Blasdel.
In D. S. Touretzky and R. Lippman, editors, Advances in Neural
Information Processing Systems 4, pp. 83-90. Morgan Kaufmann Publishers,
1992.
|
| 167. Statistical-mechanical analysis of self-organization and pattern
formation during the development of visual maps.
Klaus Obermayer, Gary G. Blasdel, and Klaus Schulten.
Physical Review A, 45:7568-7589, 1992.
|
| 165. Computational biology on massively parallel machines.
Klaus Schulten.
In Parallel Computation - Proceedings of the First
International ACPC Conference, Salzburg, Austria, pp. 391-400, New York,
1992. Springer.
|
| 164. Self-organizing maps: Stationary states, metastability and
convergence rate.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
Biological Cybernetics, 67:35-45, 1992.
|
| 163. Self-organizing maps: Ordering, convergence properties and energy
functions.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
Biological Cybernetics, 67:47-55, 1992.
|
| 162. Nuclear spin dynamics (I=1/2) under the influence of random
perturbation fields in the "strong collision" approximation.
Wolfgang R. Bauer and Klaus Schulten.
Berichte der Bunsengesellschaft - Physical Chemistry Chemical
Physics, 96:721-727, 1992.
|
| 159. Textbook: Neural Computation and Self-Organizing Maps: An
Introduction.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
Addison-Wesley, New York, revised English edition, 1992.
|
| 158. Formation of dimension-reducing somatotopic maps.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
In Samir I. Sayegh, editor, Proceedings of the Fourth Conference
on Neural Networks and Parallel Distributed Processing, pp. 115-126.
Indiana University at Fort Wayne, 1992.
|
| 157. Molecular dynamics simulation on a network of workstations using a
machine-independent parallel programming language.
Mark A. Shifman, Andreas Windemuth, Klaus Schulten, and Perry L. Miller.
Computers and Biomedical Research, 25:168-180, 1992.
(PMC: 2247565) |
| 149. "Neural gas" for vector quantization and its application to
time-series prediction.
Thomas M. Martinetz, Stanislav G. Berkovich, and Klaus Schulten.
IEEE Transactions on Neural Networks, 4:558-569, 1993.
|
| 148. A neural network for robot control: Cooperation between neural units
as a requirement for learning.
Thomas Martinetz and Klaus Schulten.
Computers & Electrical Engineering, 19:315-332, 1993.
|
| 147. Edge enhancement by diffusion in microscopic magnetic resonance
imaging.
Benno Pütz, Daniel Barsky, and Klaus Schulten.
Journal of Magnetic Resonance, 97:27-53, 1992.
|
| 142. Molecular dynamics simulations in heterogenous dielectrica and
Debye-Hückel media: Application to the protein bovine pancreatic
trypsin inhibitor.
Christoph Niedermeier and Klaus Schulten.
Molecular Simulation, 8:361-387, 1992.
|
| 129. Theory of paramagnetic contrast agents in liposome systems.
Daniel Barsky, Benno Pütz, Klaus Schulten, and Richard L. Magin.
Magnetic Resonance in Medicine, 24:1-13, 1992.
|
| 161. Edge enhancement by diffusion: Microscopic magnetic resonance imaging
of an ultra-thin glass capillary.
Benno Pütz, Daniel Barsky, and Klaus Schulten.
Chemical Physics Letters, 183:391-396, 1991.
|
| 160. Vector quantization algorithm for time series prediction and
visuo-motor control of robots.
Stanislav G. Berkovitch, Philippe Dalger, Ted Hesselroth, Thomas Martinetz,
Benoît Noël, Jörg A. Walter, and Klaus Schulten.
In W. Brauer and D. Hernandez, editors, Verteilte
Künstliche Intelligenz und kooperatives Arbeiten, volume 291 of
Informatikfachberichte, pp. 443-447. Springer, Berlin, 1991.
|
| 156. Structure of bacteriorhodopsin and in situ isomerization of
retinal: A molecular dynamics study.
Marco Nonella, Andreas Windemuth, and Klaus Schulten.
Journal Photochemistry Photobiology, 54:937-948, 1991.
|
| 155. Development and spatial structure of cortical feature maps: A model
study.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
In D. Touretzky and R. Lippman, editors, Advances in Neural
Information Processing Systems 3, pp. 11-17. Morgan Kaufmann, San Mateo CA,
1991.
|
| 154. Dynamics of synchronous neural activity in the visual cortex.
Christian Kurrer, Benno Nieswand, and Klaus Schulten.
In Teuvo Kohonen, Kai Mäkisara, Olli Simula, and Jari Kangas,
editors, Artificial Neural Networks, pp. 133-138. Elsevier, Amsterdam,
1991.
|
| 153. Industrial robot learns visuo-motor coordination by means of "neural
gas" network.
Jörg A. Walter, Thomas Martinetz, and Klaus Schulten.
In Teuvo Kohonen, Kai Mäkisara, Olli Simula, and Jari Kangas,
editors, Artificial Neural Networks, pp. 357-364. Elsevier, Amsterdam,
1991.
|
| 152. Convergence properties of self-organizing maps.
Edgar Erwin, Klaus Obermayer, and Klaus Schulten.
In Teuvo Kohonen, Kai Mäkisara, Olli Simula, and Jari Kangas,
editors, Artificial Neural Networks, pp. 409-414. Elsevier, Amsterdam,
1991.
|
| 151. A neural network model for the formation and for the spatial
structure of retinotopic maps, orientation- and ocular dominance columns.
Klaus Obermayer, Gary G. Blasdel, and Klaus Schulten.
In Teuvo Kohonen, Kai Mäkisara, Olli Simula, and Jari Kangas,
editors, Artificial Neural Networks, pp. 505-511. Elsevier, Amsterdam,
1991.
|
| 150. A "neural gas" network learns topologies.
Thomas Martinetz and Klaus Schulten.
In Teuvo Kohonen, Kai Mäkisara, Olli Simula, and Jari Kangas,
editors, Artificial Neural Networks, pp. 397-402. Elsevier, Amsterdam,
1991.
|
| 146. Coupling of protein motion to electron transfer: Molecular dynamics
and stochastic quantum mechanics study of photosynthetic reaction centers.
Klaus Schulten and Markus Tesch.
Chemical Physics, 158:421-446, 1991.
|
| 145. A model for the development of the spatial structure of retinotopic
maps and orientation columns.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
IEICE Transactions on Fundamentals of Electronics
Communications and Computer Sciences, E75-A:537-545, 1992.
Reprinted in The Principles of Organization in Organisms -
Santa Fe Institute Studies in the Sciences of Complexity, Vol. XII.
A. Baskin and J. Mittenthal, Eds. (Addison Wesley, 1991).
|
| 144. A model for synchronous activity in the visual cortex.
Christian Kurrer, Benno Nieswand, and Klaus Schulten.
In A. Babloyantz, editor, Self-Organization, Emergent
Properties, and Learning, volume 260 of NATO Science Series B:
Physics, pp. 81-95. Plenum Press, New York, 1991.
|
| 143. Molecular dynamics investigation of the interaction between DNA and
dystamycin.
Klaus Boehncke, Marco Nonella, Klaus Schulten, and Andrew H.-J. Wang.
Biochemistry, 30:5465-5475, 1991.
|
| 141. Generalized Verlet algorithm for efficient molecular dynamics
simulations with long-range interactions.
Helmut Grubmüller, Helmut Heller, Andreas Windemuth, and Klaus Schulten.
Molecular Simulation, 6:121-142, 1991.
|
| 137. Effect of noise and perturbations on limit cycle systems.
Christian Kurrer and Klaus Schulten.
Physica D, 50:311-320, 1991.
|
| 136. Self-organizing maps and adaptive filters.
Helge Ritter, Klaus Obermayer, Klaus Schulten, and Jeanne Rubner.
In J. Leo van Hemmen, Eytan Domany, and Klaus Schulten, editors,
Models of Neural Networks, Physics of Neural Networks, pp. 281-306.
Springer-Verlag, New York, 1991.
|
| 135. Stochastic dynamics simulation for macromolecules.
Andreas Windemuth and Klaus Schulten.
Beckman Institute Technical Report TB-91-19, University of Illinois,
1991.
|
| 134. Molecular dynamics simulation of electron transfer in proteins:
Theory and application to QA → QB transfer in the
photosynthetic reaction center.
Marco Nonella and Klaus Schulten.
Journal of Physical Chemistry, 95:2059-2067, 1991.
|
| 127. Molecular dynamics simulation on the Connection Machine.
Andreas Windemuth and Klaus Schulten.
Molecular Simulation, 5:353-361, 1991.
|
| 126. Semistochastic approach to many electron systems.
M. K. Grossjean, Michael F. Grossjean, Klaus Schulten, and Paul Tavan.
Journal of Chemical Physics, 97:1865-1875, 1992.
|
| 125. Theory of contrast agents in magnetic resonance imaging: Coupling of
spin relaxation and transport.
Wolfgang R. Bauer and Klaus Schulten.
Magnetic Resonance in Medicine, 26:16-39, 1992.
|
| 123. Chromophore-protein interactions and the function of the
photosynthetic reaction center: A molecular dynamics study.
Herbert Treutlein, Klaus Schulten, Axel Brünger, Martin Karplus,
J. Deisenhofer, and H. Michel.
Proceedings of the National Academy of Sciences, USA,
89:75-79, 1992.
|
| 120. Propagation of chemical waves in discrete excitable media:
Anisotropic and isotropic wave fronts.
Christian Kurrer and Klaus Schulten.
In A. V. Holden, M. Markus, and H. G. Othmer, editors, Nonlinear
Wave Processes in Excitable Media, volume 244 of NATO Science
Series B: Physics, pp. 489-500. Plenum Press, New York, 1991.
|
| 140. Simulation of self-organizing neural nets: A comparision between a
transputer ring and a Connection Machine CM-2.
Klaus Obermayer, Helmut Heller, Helge Ritter, and Klaus Schulten.
In Alan S. Wagner, editor, NATUG 3: Transputer Research and
Applications 3, pp. 95-106, Amsterdam, 1990. North American Transputer
Users Group, IOS Press.
|
| 139. Molecular dynamics simulations on a systolic ring of transputers.
Klaus Boehncke, Helmut Heller, Helmut Grubmüller, and Klaus Schulten.
In Alan S. Wagner, editor, NATUG 3: Transputer Research and
Applications 3, pp. 83-94, Amsterdam, 1990. North American Transputer Users
Group, IOS Press.
|
| 138. A principle for the formation of the spatial structure of cortical
feature maps.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
87:8345-8349, 1990.
(PMC: 54952) |
| 133. Large-scale simulations of self-organizing neural networks on
parallel computers: Application to biological modelling.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
Parallel Computing, 14:381-404, 1990.
|
| 132. Hierarchical neural net for learning control of a robot's arm and
gripper.
Thomas Martinetz and Klaus Schulten.
In International Joint Conference on Neural Networks, San Diego,
California, volume 2, pp. 747-752. The Institute of Electrical and
Electronics Engineers, New York, 1990.
|
| 131. A neural network model for the formation of topographic maps in the
CNS: Development of receptive fields.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
In International Joint Conference on Neural Networks, San Diego,
California, volume 2, pp. 423-429. The Institute of Electrical and
Electronics Engineers, New York, 1990.
|
| 130. Non-linear prediction with self-organizing maps.
Jörg A. Walter, Helge Ritter, and Klaus Schulten.
In International Joint Conference on Neural Networks, San Diego,
California, volume 1, pp. 589-594. The Institute of Electrical and
Electronics Engineers, New York, 1990.
|
| 128. A simulated cooling process for proteins.
Markus Tesch and Klaus Schulten.
Chemical Physics Letters, 169:97-102, 1990.
|
| 124. Quantum chemical vibrational analysis of the chromophore of
bacteriorhodopsin.
Michael F. Grossjean, Paul Tavan, and Klaus Schulten.
Journal of Physical Chemistry, 94:8059-8069, 1990.
|
| 122. Textbook: Neuronale Netze: Eine Einführung in die
Neuroinformatik selbstorganisierender Abbildungen.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
Addison-Wesley, Bonn, second enlarged edition, 1990.
|
| 121. Micellar radical pair decay.
Robert Bittl, Klaus Schulten, and Nick Turro.
Journal of Chemical Physics, 93:8260-8269, 1990.
|
| 119. A self-organizing network for complete feature extraction.
Jeanne Rubner, Klaus Schulten, and Paul Tavan.
In R. Eckmiller, G. Hartmann, and G. Hauske, editors, Parallel
Processing in Neural Systems and Computers, pp. 365-368. Elsevier,
Amsterdam, 1990.
|
| 118. Hierarchical spin model for stereo interpretation using phase
sensitive detectors.
Robert Divko and Klaus Schulten.
In R. Eckmiller, G. Hartmann, and G. Hauske, editors, Parallel
Processing in Neural Systems and Computers, pp. 335-338. Elsevier,
Amsterdam, 1990.
|
| 117. Learning of visuo motor-coordination of a robot arm with redundant
degrees of freedom.
Thomas Martinetz, Helge Ritter, and Klaus Schulten.
In R. Eckmiller, G. Hartmann, and G. Hauske, editors, Parallel
Processing in Neural Systems and Computers, pp. 431-434. Elsevier,
Amsterdam, 1990.
|
| 116. Large-scale simulation of a self-organizing neural network: Formation
of a somatotopic map.
Klaus Obermayer, Helge Ritter, and Klaus Schulten.
In R. Eckmiller, G. Hartmann, and G. Hauske, editors, Parallel
Processing in Neural Systems and Computers, pp. 71-74. Elsevier, Amsterdam,
1990.
|
| 115. Development of feature detectors by self-organization: A network
model.
Jeanne Rubner and Klaus Schulten.
Biological Cybernetics, 62:193-199, 1990.
|
| 114. Three-dimensional neural net for learning visuo-motor coordination of
a robot arm.
Thomas Martinetz, Helge Ritter, and Klaus Schulten.
IEEE Transactions on Neural Networks, 1:131-136, 1990.
|
| 113. Biradical spin dynamics with distance-dependent exchange interaction
and electron transfer efficiency.
Robert Bittl and Klaus Schulten.
Chemical Physics Letters, 173:387-392, 1990.
|
| 111. Molecular dynamics simulation on a parallel computer.
Helmut Heller, Helmut Grubmüller, and Klaus Schulten.
Molecular Simulation, 5:133-165, 1990.
|
| 110. Textbook: Neuronale Netze: Eine Einführung in die
Neuroinformatik selbstorganisierender Abbildungen.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
Addison-Wesley, Bonn, first edition, 1990.
|
| 109. Kohonen's self-organizing map for modeling the formation of the
auditory cortex of a bat.
Thomas Martinetz, Helge Ritter, and Klaus Schulten.
In R. Pfeifer, Z. Schreter, F. Fogelman-Soulié, and L. Steels,
editors, Connectionism in Perspective, pp. 403-412. North-Holland,
Amsterdam, 1989.
|
| 108. 3D-neural-net for learning visuomotor-coordination of a robot arm.
Thomas Martinetz, Helge Ritter, and Klaus Schulten.
In Proceedings of the International Joint Conference on Neural
Networks, Washington, volume 2, pp. 351-356, San Diego, 1989. The Institute
of Electrical and Electronics Engineers.
|
| 107. On sparsely coded associative memories.
Joachim Buhmann, Robert Divko, and Klaus Schulten.
In L. Personnaz and G. Dreyfus, editors, Neural Networks: From
Models to Applications, N'EURO '88, pp. 360-371. EZIDET, Paris,
1989.
|
| 112. Mathematica: Mathematik auf Mikrocomputern.
Markus van Almsick and Klaus Schulten.
MC-Computermagazin, 11:42-59, 1989.
|
| 106. Topology-conserving maps for motor control.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
In L. Personnaz and G. Dreyfus, editors, Neural Networks: From
Models to Applications, N'EURO '88, pp. 579-591. EZIDET, Paris,
1989.
|
| 105. A regularized approach to color constancy.
Jeanne Rubner and Klaus Schulten.
Biological Cybernetics, 61:29-36, 1989.
|
| 104. Topology-conserving maps for learning visuo-motor-coordination.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
Neural Networks, 2:159-168, 1989.
|
| 103. Wie neuronale Netwerke Roboter steuern können.
Helge Ritter, Thomas Martinetz, and Klaus Schulten.
MC-Computermagazin, 2:48-61, 1989.
|
| 102. Can normal mode analysis reveal the geometry of the L550
chromophore of bacteriorhodopsin?
Michael F. Grossjean, Paul Tavan, and Klaus Schulten.
European Biophysics Journal, 16:341-349, 1989.
|
| 97. Associative memory with high information content.
Joachim Buhmann, Robert Divko, and Klaus Schulten.
Physical Review A, 39:2689-2692, 1989.
|
| 94. A static ensemble approximation for stochastically modulated quantum
systems.
Robert Bittl and Klaus Schulten.
Journal of Chemical Physics, 90:1794-1803, 1989.
|
| 101. Molecular dynamics simulation of the primary processes in the
Photosynthetic reaction center of Rhodopseudomonas
viridis.
Herbert Treutlein, Christoph Niedermeier, Klaus Schulten, J. Deisenhofer,
H. Michel, Axel Brünger, and Martin Karplus.
In A. Pullman et al., editors, Transport Through Membranes:
Carriers, Channels and Pumps, pp. 513-525. Kluwer Academic Publishers,
Dordrecht, 1988.
|
| 100. Eine Cray für 100.000 DM.
Helmut Grubmüller, Helmut Heller, and Klaus Schulten.
MC-Computermagazin, 11:48-64, 1988.
|
| 99. Invariant pattern recognition by means of fast synaptic plasticity.
Joachim Buhmann and Klaus Schulten.
In IEEE International Conference on Neural Networks, San Diego,
California, July 24-27, 1988, volume 1, pp. 125-132, New York, 1988. The
Institute of Electrical and Electronics Engineers.
|
| 98. Kohonen's self-organizing maps: Exploring their computational
capabilities.
Helge Ritter and Klaus Schulten.
In IEEE International Conference on Neural Networks, San Diego,
California, July 24-27, 1988, volume 1, pp. 109-116, New York, 1988. The
Institute of Electrical and Electronics Engineers.
|
| 96. Mean relaxation time approximation for dynamical correlation
functions in stochastic systems near instabilities: II. The single mode
laser.
Walter Nadler and Klaus Schulten.
Zeitschrift für Physik, 72:535-543, 1988.
|
| 95. Convergence properties of Kohonen's topology conserving maps:
Fluctuations, stability and dimension selection.
Helge Ritter and Klaus Schulten.
Biological Cybernetics, 60:59-71, 1988.
|
| 93. Eine Computersimulation künstlicher Wesen - Experimente in
einer Welt synthetischer Psychologie.
Klaus Boehncke, Christoph Köhler, Georg Meyer-Berg, and Klaus Schulten.
MC-Computermagazin, 7:34-48, 1988.
|
| 92. Length dependence of the magnetic field modulated triplet yield of
photogenerated biradicals.
Robert Bittl and Klaus Schulten.
Chemical Physics Letters, 146:58-62, 1988.
|
| 91. Electrostatic control of electron transfer in the photosynthetic
reaction center of Rhodopseudomonas viridis.
Herbert Treutlein, Klaus Schulten, Christoph Niedermeier, J. Deisenhofer,
H. Michel, and D. Devault.
In J. Breton and A. Verméglio, editors, The Photosynthetic
Bacterial Reaction Center: Structure and Dynamics, volume 149 of NATO
Science Series A: Life Sciences, pp. 369-377. Plenum, New York, 1988.
|
| 90. Molecular dynamics simulation of the primary processes in the
photosynthetic reaction center of Rhodopseudomonas
viridis.
Herbert Treutlein, Klaus Schulten, J. Deisenhofer, H. Michel, Axel Brünger,
and Martin Karplus.
In J. Breton and A. Verméglio, editors, The Photosynthetic
Bacterial Reaction Center: Structure and Dynamics, volume 149 of NATO
Science Series A: Life Sciences, pp. 139-150. Plenum, New York, 1988.
|
| 89. Generalized moment expansion of dynamic correlation functions in
finite Ising systems.
Hans-Ulrich Bauer, Klaus Schulten, and Walter Nadler.
Physical Review B, 38:445-458, 1988.
|
| 88. Quasiparticle excitations in polyenes and polyacetylene.
Paul Tavan and Klaus Schulten.
In A. J. Heeger, J. Orenstein, and D. Ulrich, editors, Nonlinear
Optical Properties of Polymers, volume 109 of Symposium Proceedings,
pp. 163-170. Materials Research Society, Pittsburgh, 1988.
|
| 87. "Molecular Design" - Simulation und Graphik von Biomolekülen.
Herbert Treutlein, Andreas Windemuth, and Klaus Schulten.
MC-Computermagazin, 1:46-57, 1988.
|
| 86. Storing sequences of biased patterns in neural networks with
stochastic dynamics.
Joachim Buhmann and Klaus Schulten.
In R. Eckmiller and Ch. von der Malsburg, editors, Neural
Computers, Computer and Systems Sciences, pp. 231-242. Springer, 1988.
|
| 85. Extending Kohonen's self-organizing mapping algorithm to learn
ballistic movements.
Helge Ritter and Klaus Schulten.
In R. Eckmiller and Ch. von der Malsburg, editors, Neural
Computers, volume 41 of NATO Science Series F: Computer and Systems
Sciences, pp. 393-406. Springer-Verlag, 1988.
|
| 84. Spectroscopic determinants in the reaction center of
Rhodopseudomonas viridis.
Joseph Eccles, Barry Honig, and Klaus Schulten.
Biophysical Journal, 53:137-144, 1988.
(PMC: 1330134) |
| 83. Physik und Gehirn - Wie dynamische Modelle von Nervennetzen
natürliche Intelligenz erklären.
Joachim Buhmann, Robert Divko, Helge Ritter, and Klaus Schulten.
MC-Computermagazin, 9:108-120, 1987.
|
| 82. Molecular and stochastic dynamics of proteins.
Walter Nadler, Axel Brünger, Klaus Schulten, and Martin Karplus.
Proceedings of the National Academy of Sciences, USA,
84:7933-7937, 1987.
(PMC: 299450) |
| 81. Ordnung aus Chaos, Vernunft aus Zufall - Physik biologischer und
digitaler Informationsverarbeitung.
Klaus Schulten.
In B.-O. Küppers, editor, Ordnung aus dem Chaos, pp.
243-268. Piper Verlag, Munich, 1987.
|
| 80. Brownian dynamics simulation of diffusion to irregular bodies.
Kim Sharp, Richard Fine, Klaus Schulten, and Barry Honig.
Physical Chemistry, 91:3624-3631, 1987.
|
| 79. Electronic excitations in finite and infinite polyenes.
Paul Tavan and Klaus Schulten.
Physical Review B, 36:4337-4358, 1987.
|
| 78. Noise-driven temporal association in neural networks.
Joachim Buhmann and Klaus Schulten.
Europhysics Letters, 4:1205-1209, 1987.
|
| 77. Influence of noise on the function of a "physiological" neural
network.
Joachim Buhmann and Klaus Schulten.
Biological Cybernetics, 56:313-327, 1987.
|
| 76. Physicists explore human and artificial intelligence.
Joachim Buhmann, Robert Divko, Helge Ritter, and Klaus Schulten.
In Structure and Dynamics of Nucleic Acids, Proteins and
Membranes, pp. 301-328. Plenum Press, 1986.
|
| 75. Planning a dynamic trajectory via path finding in discretized phase
space.
Helge Ritter and Klaus Schulten.
In Parallel Processing: Logic, Organization, and Technology,
volume 253 of Lecture Notes in Computer Science, pp. 29-39. Springer,
1987.
|
| 74. The low-lying electronic excitations in long polyenes: A
PPP-MRD-CI study.
Paul Tavan and Klaus Schulten.
Journal of Chemical Physics, 85:6602-6609, 1986.
|
| 73. Stochastic spin models for pattern recognition.
Robert Divko and Klaus Schulten.
In J. S. Denker, editor, Neural Networks for Computing, pp.
129-134. American Institute of Physics Publication, Conference Proceedings
151, 1986.
|
| 72. Topology conserving mappings for learning motor tasks.
Helge Ritter and Klaus Schulten.
In J. S. Denker, editor, Neural networks for computing, pp.
376-380. American Institute of Physics publication, conference proceedings
151, 1986.
|
| 71. Influence of noise on the behaviour of an autoassociative neural
network.
Joachim Buhmann and Klaus Schulten.
In J. S. Denker, editor, Neural Networks for Computing, pp.
71-76. American Institute of Physics Publication, Conference Proceedings
151, 1986.
|
| 70. Model for a physiological magnetic compass.
Klaus Schulten and Andreas Windemuth.
In G. Maret, N. Boccara, and J. Kiepenheuer, editors,
Biophysical Effects of Steady Magnetic Fields, volume 11 of Proceedings
in Physics, pp. 99-106. Springer, Berlin, 1986.
|
| 69. Magnetic field effects on radical pair processes in chemistry and
biology.
Klaus Schulten.
In J. H. Bernhard, editor, Biological Effects of Static and
Extremely Low Frequency Magnetic Fields, pp. 133-140. MMV Medizin Verlag,
Munich, 1986.
|
| 68. Study of polymer dynamics by magnetic field dependent biradical
reactions.
Robert Bittl and Klaus Schulten.
In G. Maret, N. Boccara, and J. Kiepenheuer, editors,
Biophysical Effects of Steady Magnetic Fields, volume 11 of Proceedings
in Physics, pp. 90-98. Springer, Berlin, 1986.
|
| 67. Trans-cis isomerization of retinal and a mechanism for ion
translocation in halorhodopsin.
Dieter Oesterhelt, P. Hegemann, Paul Tavan, and Klaus Schulten.
European Biophysics Journal, 14:123-129, 1986.
|
| 66. A physiological neural network as an autoassociative memory.
Joachim Buhmann and Klaus Schulten.
In E. Bienenstock, F. Fogelman, and G. Weisbuch, editors,
Disordered Systems and Biological Organization, pp. 273-279. Springer,
1986.
|
| 65. Associative recognition and storage in a model network of
physiological neurons.
Joachim Buhmann and Klaus Schulten.
Biological Cybernetics, 54:319-335, 1986.
|
| 64. Evidence for a 13,14-cis cycle in bacteriorhodopsin.
Paul Tavan and Klaus Schulten.
Biophysical Journal, 50:81-89, 1986.
(PMC: 1329661) |
| 63. Continuous fluorescence microphotolysis by a sin2 kx grating.
Klaus Schulten.
Chemical Physics Letters, 124:230-236, 1986.
|
| 62. On the stationary state of Kohonen's self-organizing sensory
mapping.
Helge Ritter and Klaus Schulten.
Biological Cybernetics, 54:99-106, 1986.
|
| 61. Probing the dynamics of a polymer with paramagnetic end groups by
magnetic fields.
Klaus Schulten and Robert Bittl.
Journal of Chemical Physics, 84:5155-5161, 1986.
|
| 60. Generalized moment expansion for observables of stochastic processes
in dimensions d > 1: Application to Mössbauer spectra of proteins.
Walter Nadler and Klaus Schulten.
Journal of Chemical Physics, 84:4015-4025, 1986.
|
| 59. Noise-induced neural impulses.
Herbert Treutlein and Klaus Schulten.
European Biophysics Journal, 13:355-365, 1986.
|
| 58. Proton conduction through proteins: An overview of theoretical
principles and applications.
Zan Schulten and Klaus Schulten.
Methods in Enzymology, 127:419-438, 1986.
|
| 57. Neuro-kybernetik und künstliche Intelligenz.
Joachim Buhmann, Helge Ritter, and Klaus Schulten.
Computerwoche, 25, 1985.
|
| 56. Electron conduction along aliphatic chains.
Robert Bittl, Herbert Treutlein, and Klaus Schulten.
In M. Michel-Beyerle, editor, Antennas and Reaction Centers of
Photosynthetic Bacteria - Structure, Interaction and Dynamics, pp.
264-276. Springer, 1985.
|
| 55. Single-cell flux measurement by continuous fluorescence
microphotolysis.
M. Scholz, Klaus Schulten, and Reiner Peters.
European Biophysics Journal, 13:37-44, 1985.
|
| 54. Mean relaxation time approximation for dynamical correlation
functions in stochastic systems near instabilities.
Walter Nadler and Klaus Schulten.
Zeitschrift für Physik B, 59:53-61, 1985.
|
| 53. Noise induced limit cycles of the Bonhoeffer-van der Pol model
of neural pulses.
Herbert Treutlein and Klaus Schulten.
Berichte der Bunsengesellschaft - Physical Chemistry Chemical
Physics, 89:710-718, 1985.
|
| 52. A model for the lateral diffusion of `stiff' chains in a lipid
bilayer.
Walter Nadler, Paul Tavan, and Klaus Schulten.
European Biophysics Journal, 12:25-31, 1985.
|
| 51. Generalized moment expansion for Brownian relaxation processes.
Walter Nadler and Klaus Schulten.
Journal of Chemical Physics, 82:151-160, 1985.
|
| 50. The effect of intramolecular paramagnetic-diamagnetic exchange on
the magnetic field effect of radical pair recombination.
Klaus Schulten.
Journal of Chemical Physics, 82:1312-1316, 1985.
|
| 49. Continuous fluorescence microphotolysis to observe lateral diffusion
in membranes: Theoretical methods and applications.
Axel Brünger, Reiner Peters, and Klaus Schulten.
Journal of Chemical Physics, 82:2147-2160, 1985.
|
| 48. Substituents at the C13 position of retinal and their
influence on the function of bacteriorhodopsin.
Paul Tavan, Klaus Schulten, Wolfgang Gärtner, and Dieter Oesterhelt.
Biophysical Journal, 47:349-356, 1985.
(PMC: 1435211) |
| 47. Model for the resistance of the proton channel formed by the
proteolipid of ATPase.
Zan Schulten and Klaus Schulten.
European Biophysics Journal, 11:149-155, 1985.
|
| 46. The effect of protonation and electrical interactions on the
stereochemistry of retinal Schiff bases.
Paul Tavan, Klaus Schulten, and Dieter Oesterhelt.
Biophysical Journal, 47:415-430, 1985.
(PMC: 1435223) |
| 45. Magnetfeldeffekte in Chemie und Biologie.
Klaus Schulten and Albert Weller.
Die Umschau, 25/26:779-783, 1984.
|
| 44. The effect of protonation on the thermal isomerization of
stilbazolium betaines.
Paul Tavan and Klaus Schulten.
Chemical Physics Letters, 110:191-195, 1984.
|
| 43. Theory of Mössbauer spectra of proteins fluctuating between
conformational substates.
Walter Nadler and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
81:5719-5723, 1984.
(PMC: 391782) |
| 42. An isomerization model for the pump cycle of bacteriorhodopsin.
Klaus Schulten, Zan Schulten, and Paul Tavan.
In L. Bolis, E. J. M. Helmreich, and H. Passow, editors,
Information and Energy Transduction in Biological Membranes, pp. 113-131.
Allan R. Liss, Inc., New York, 1984.
|
| 41. Generalized moment description of Brownian dynamics in biological
systems.
Klaus Schulten, Axel Brünger, Walter Nadler, and Zan Schulten.
In E. Frehland, editor, Synergetics - From Microscopic to
Macroscopic Order, pp. 80-89. Springer, 1984.
|
| 40. Ensemble averaged spin pair dynamics of doublet and triplet
molecules.
Klaus Schulten.
Journal of Chemical Physics, 80:3668-3679, 1984.
|
| 39. A network thermodynamic investigation of stationary and
non-stationary proton transport through proteins.
Axel Brünger, Zan Schulten, and Klaus Schulten.
Zeitschrift für Physikalische Chemie, NF136:1-63, 1983.
|
| 38. Ensemble averaged spin pair dynamics of doublet and triplet
molecules.
Klaus Schulten.
In P. Reineker, H. Haken, and H. C. Wolf, editors, Organic
Molecular Aggregates, pp. 76-87. Springer, 1983.
|
| 37. Generalized moment expansion for the Mössbauer spectrum of
Brownian particles.
Walter Nadler and Klaus Schulten.
Physical Review Letters, 51:1712-1715, 1983.
|
| 36. Extended Brownian dynamics: II. Reactive, nonlinear diffusion.
Gene Lamm and Klaus Schulten.
Journal of Chemical Physics, 78:2713-2734, 1983.
|
| 35. Linear polyene electronic structure and potential surfaces.
Bruce S. Hudson, Bryan E. Kohler, and Klaus Schulten.
In Edward C. Lim, editor, Excited States, volume 6, pp. 1-95.
Academic Press, New York, 1982.
|
| 34. Magnetic field effects in chemistry and biology.
Klaus Schulten.
In J. Treusch, editor, Festkörperprobleme, volume 22, pp.
61-83. Vieweg, Braunschweig, 1982.
|
| 33. Extended Brownian dynamics approach to diffusion-controlled
processes.
Gene Lamm and Klaus Schulten.
Journal of Chemical Physics, 75:365-371, 1981.
|
| 32. Continuous fluorescence microphotolysis: A sensitive method for study
of diffusion processes in single cells.
Reiner Peters, Axel Brünger, and Klaus Schulten.
Proceedings of the National Academy of Sciences, USA,
78:962-966, 1981.
(PMC: 319925) |
| 31. Dynamics of reactions involving diffusive barrier crossing.
Klaus Schulten, Zan Schulten, and Attila Szabo.
Journal of Chemical Physics, 74:4426-4432, 1981.
|
| 30. The spectra of carbonium ions, cyanine dyes, and protonated Schiff
base polyenes.
Klaus Schulten, Uri Dinur, and Barry Honig.
Journal of Chemical Physics, 73:3927-3935, 1980.
|
| 29. On the nature of excited electronic states in cyanine dyes:
Implications for visual pigment spectra.
Uri Dinur, Barry Honig, and Klaus Schulten.
Chemical Physics Letters, 72:493-497, 1980.
|
| 28. First passage time approach to diffusion controlled reactions.
Attila Szabo, Klaus Schulten, and Zan Schulten.
Journal of Chemical Physics, 72:4350-4357, 1980.
|
| 27. An efficient approach to CI: General matrix element formulas for
spin-coupled particle-hole excitations.
Paul Tavan and Klaus Schulten.
Journal of Chemical Physics, 72:3547-3576, 1980.
|
| 26. Reactions governed by a binomial redistribution process. The
Ehrenfest urn problem.
Klaus Schulten, Zan Schulten, and Attila Szabo.
Physica, 100A:599-614, 1980.
|
| 25. Proton conduction in linear hydrogen-bonded systems.
Ernst-Walter Knapp, Klaus Schulten, and Zan Schulten.
Chemical Physics, 46:215-229, 1980.
|
| 24. Magnetic field effect on the hyperfine-induced electron spin motion
in radicals undergoing diamagnetic-paramagnetic exchange.
Ernst-Walter Knapp and Klaus Schulten.
Journal of Chemical Physics, 71:1878-1883, 1979.
|
| 23. Recombination of radical pairs in high magnetic fields: A path
integral-Monte Carlo treatment.
Klaus Schulten and Irving R. Epstein.
Journal of Chemical Physics, 71:309-316, 1979.
|
| 22. Correlation effects in the spectra of polyacenes.
Paul Tavan and Klaus Schulten.
Journal of Chemical Physics, 70:5414-5421, 1979.
|
| 21. The 21Ag - 11Bu energy gap in the polyenes: An extended
configuration interaction study.
Paul Tavan and Klaus Schulten.
Journal of Chemical Physics, 70:5407-5413, 1979.
|
| 20. Coupling of stereochemistry and proton donor-acceptor properties of
a Schiff base: A model of a light-driven proton pump.
G. Orlandi and Klaus Schulten.
Chemical Physics Letters, 64:370-374, 1979.
|
| 19. A biomagnetic sensory mechanism based on magnetic field modulated
coherent electron spin motion.
Klaus Schulten, Charles E. Swenberg, and Albert Weller.
Zeitschrift für Physikalische Chemie, NF111:1-5, 1978.
|
| 18. An isomerization model for the photocycle of bacteriorhodopsin.
Klaus Schulten.
In S. R. Caplan and M. Ginzburg, editors, Energetics and
Structure of Halophilic Organisms, pp. 331-334. Elsevier, 1978.
|
| 17. Exploring fast electron transfer processes by magnetic fields.
Klaus Schulten and Albert Weller.
Biophysical Journal, 24:295-305, 1978.
(PMC: 1473906) |
| 16. Semiclassical description of electron spin motion in radicals
including the effect of electron hopping.
Klaus Schulten and Peter G. Wolynes.
Journal of Chemical Physics, 68:3292-3297, 1978.
|
| 15. The `phantom' photochemical singlet state of stilbene and its
diphenylpolyene relative.
Paul Tavan and Klaus Schulten.
Chemical Physics Letters, 56:200-204, 1978.
|
| 14. Electron transfer and spin exchange contributing to the magnetic
field dependence of the primary photochemical reaction of bacterial
photosynthesis.
Hans-Joachim Werner, Klaus Schulten, and Albert Weller.
Biochimica et Biophysica Acta, 502:255-268, 1978.
|
| 13. A mechanism for the light-driven proton pump of
Halobacterium halobium.
Klaus Schulten and Paul Tavan.
Nature, 272:85-86, 1978.
|
| 12. Renormalized configuration interaction method for electron
correlation in the excited states of polyenes.
I. Ohmine, Martin Karplus, and Klaus Schulten.
Journal of Chemical Physics, 68:2298-2318, 1978.
|
| 11. Theory of the magnetic field modulated geminate recombination of
radical ion pairs in polar solvents: Application to the
pyrene-N,N-dimethylaniline system.
Hans-Joachim Werner, Zan Schulten, and Klaus Schulten.
Journal of Chemical Physics, 67:646-663, 1977.
|
| 10. The generation, diffusion, spin motion, and recombination of radical
pairs in solution in the nanosecond time domain.
Zan Schulten and Klaus Schulten.
Journal of Chemical Physics, 66:4616-4634, 1977.
|
| 9. Quantum mechanical propensity rules for the transfer of angular
momentum in three-atom reactions.
Klaus Schulten.
Berichte der Bunsengesellschaft - Physical Chemistry Chemical
Physics, 81:166-168, 1977.
|
| 8. Magnetic field dependence of the geminate recombination of radical
ion pairs in polar solvents.
Klaus Schulten, H. Staerk, Albert Weller, Hans-Joachim Werner, and B. Nickel.
Zeitschrift für Physikalische Chemie, NF101:371-390, 1976.
|
| 7. Recursive evaluation of 3j- and 6j-coefficients.
Klaus Schulten and Roy G. Gordon.
Computational Physics Communications, 11:269-278, 1976.
|
| 6. Quantum theory of angular momentum coupling in reactive collisions.
Klaus Schulten and Roy G. Gordon.
Journal of Chemical Physics, 64:2918-2938, 1976.
|
| 5. Correlation effects in the spectra of polyenes.
Klaus Schulten, I. Ohmine, and Martin Karplus.
Journal of Chemical Physics, 64:4422-4441, 1976.
|
| 4. Semiclassical approximation to 3j- and 6j-coefficients for
quantum-mechanical coupling of angular momenta.
Klaus Schulten and Roy G. Gordon.
Journal of Mathematical Physics, 16:1971-1988, 1975.
|
| 3. Exact recursive evaluation of 3j- and 6j-coefficients for
quantum-mechanical coupling of angular momenta.
Klaus Schulten and Roy G. Gordon.
Journal of Mathematical Physics, 16:1961-1970, 1975.
|
| 2. Possible influence of a low-lying "covalent" excited state on the
absorption spectrum and photoisomerization of 11-cis retinal.
Robert R. Birge, Klaus Schulten, and Martin Karplus.
Chemical Physics Letters, 31:451-454, 1975.
|
| 1. On the origin of a low-lying forbidden transition in polyenes and
related molecules.
Klaus Schulten and Martin Karplus.
Chemical Physics Letters, 14:305-309, 1972.
|
| 379. Conformational model of the Holliday junction transition deduced
from molecular dynamics simulations.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Nucleic Acids Research, 32:6683-6695, 2004.
(PMC: 545448) |
| 10001. NAMD: Biomolecular simulation on thousands of processors.
James Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant Kale.
In Proceedings of the IEEE/ACM SC2002 Conference, Technical
Paper 277, pp. 1-18. IEEE Press, Baltimore, Maryland, 2002.
|
