|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 648. Die Geheimnisse des Lebens berechnen.
Till Rudack, Juan Perilla, and Klaus Schulten.
Spektrum der Wissenschaft, 11:86-95, November 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.
|
| 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).
|
| 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.
|
| 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.
|
| 639. Synaptotagmin's role in neurotransmitter release likely involves
Ca2+-induced conformational transition.
Zhe Wu and Klaus Schulten.
Biophysical Journal, 107:1156-1166, 2014.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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).
|
| 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.
|
| 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).
|
| 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.
|
| 615. A computational kinetic model of diffusion for molecular systems.
Ivan Teo and Klaus Schulten.
Journal of Chemical Physics, 139:121929, 2013.
(15 pages).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| |
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 551. Improved resolution of tertiary structure elasticity in muscle
protein.
Jen Hsin and Klaus Schulten.
Biophysical Journal, 100:L22-L24, 2011.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 527. Challenges in protein folding simulations.
Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten.
Nature Physics, 6:751-758, 2010.
|
| 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).
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 506. Discovery through the computational microscope.
Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, and Klaus Schulten.
Structure, 17:1295-1306, 2009.
|
| 505. Membrane-bending mechanism of amphiphysin N-BAR domains.
Anton Arkhipov, Ying Yin, and Klaus Schulten.
Biophysical Journal, 97:2727-2735, 2009.
|
| 504. Common structural transitions in explicit-solvent simulations of
villin headpiece folding.
Peter L. Freddolino and Klaus Schulten.
Biophysical Journal, 97:2338-2347, 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 496. Simulations of membrane tubulation by lattices of amphiphysin N-BAR
domains.
Ying Yin, Anton Arkhipov, and Klaus Schulten.
Structure, 17:882-892, 2009.
|
| 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.
|
| 494. Force field bias in protein folding simulations.
Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten.
Biophysical Journal, 96:3772-3780, 2009.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 478. Four-scale description of membrane sculpting by BAR domains.
Anton Arkhipov, Ying Yin, and Klaus Schulten.
Biophysical Journal, 95:2806-2821, 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 458. Diffusion of glycerol through Escherichia Coli
aquaglyceroporin GlpF.
Jerome Henin, Emad Tajkhorshid, Klaus Schulten, and Christophe Chipot.
Biophysical Journal, 94:832-839, 2008.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 450. Structural determinants of lateral gate opening in the protein
translocon.
James Gumbart and Klaus Schulten.
Biochemistry, 46:11147-11157, 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.
|
| 448. How directional translocation is regulated in a DNA helicase motor.
Jin Yu, Taekjip Ha, and Klaus Schulten.
Biophysical Journal, 93:3783-3797, 2007.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 424. Dynamics of K+ ion conduction through Kv1.2.
Fatemeh Khalili-Araghi, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 91:L72-L74, 2006.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 412. Onset of anthrax toxin pore formation.
Mu Gao and Klaus Schulten.
Biophysical Journal, 90:3267-3279, 2006.
|
| 410. Molecular dynamics studies of the archaeal translocon.
James Gumbart and Klaus Schulten.
Biophysical Journal, 90:2356-2367, 2006.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 401. Binding dynamics of isolated nucleoporin repeat regions to
importin-β.
Timothy A. Isgro and Klaus Schulten.
Structure, 13:1869-1879, 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 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.
|
| 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.
|
| 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.
|
| 365. Complementarities and convergence of results in bacteriorhodopsin
trimer simulations.
Jerome Baudry, Emad Tajkhorshid, and Klaus Schulten.
Biophysical Journal, 87:1394-1395, 2004.
|
| 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.
|
| 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.
|
| 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.
|
| 357. Lipid bilayer pressure profiles and mechanosensitive channel gating.
Justin Gullingsrud and Klaus Schulten.
Biophysical Journal, 86:3496-3509, 2004.
|
| 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.
|
| 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.
|
| 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.
|
| 349. Structural basis for cooperative DNA binding by CAP and
Lac repressor.
Alexander Balaeff, L. Mahadevan, and Klaus Schulten.
Structure, 12:123-132, 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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).
|
| 318. The mechanism of glycerol conduction in aquaglyceroporins.
Morten Ø. Jensen, Emad Tajkhorshid, and Klaus Schulten.
Structure, 9:1083-1093, 2001.
|
| 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.
|
| 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.
|
| 308. Structural determinants of MscL gating studied by molecular
dynamics simulations.
Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten.
Biophysical Journal, 80:2074-2081, 2001.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 234. Photoproducts of bacteriorhodopsin mutants: A molecular dynamics
study.
William Humphrey, Ernst Bamberg, and Klaus Schulten.
Biophysical Journal, 72:1347-1356, 1997.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 216. Molecular dynamics study of the M412 intermediate of
bacteriorhodopsin.
Dong Xu, Mordechai Sheves, and Klaus Schulten.
Biophysical Journal, 69:2745-2760, 1995.
|
| 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.
|
| 209. Molecular dynamics study of glucocorticoid receptor-DNA binding.
Thomas C. Bishop and Klaus Schulten.
PROTEINS: Structure, Function, and Genetics, 24:115-133, 1996.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 193. Molecular dynamics study of a membrane-water interface.
Feng Zhou and Klaus Schulten.
Journal of Physical Chemistry, 99:2194-2208, 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.
|
| 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.
|
| 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.
|
| 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.
|
| 169. Molecular dynamics study of the proton pump cycle of
bacteriorhodopsin.
Feng Zhou, Andreas Windemuth, and Klaus Schulten.
Biochemistry, 32:2291-2306, 1993.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
|
| 128. A simulated cooling process for proteins.
Markus Tesch and Klaus Schulten.
Chemical Physics Letters, 169:97-102, 1990.
|
| 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.
|
| 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.
|
| 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.
|
| 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.
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