|
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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.
|
| 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.
|
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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.
|
| 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) |
| 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) |
| 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) |
| 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) |
| 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.
|
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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.
|
| 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.
(PMC: PMC4266597) |
| 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).
|
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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.
|
| 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) |
| 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) |
| 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) |
| 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.
(PMC: PMC3974213) |
| 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) |
| 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.
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