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Klaus Schulten - Publications

Affiliations: 
University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
Area:
theoretical biophysics
Website:
http://www.chemistry.illinois.edu/faculty/Klaus_Schulten.html
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337 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Misra SK, Wu Z, Ostadhossein F, Ye M, Boateng K, Schulten K, Tajkhorshid E, Pan D. Pro-nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-Cancer Therapy. Acs Applied Materials & Interfaces. PMID 31013055 DOI: 10.1021/acsami.9b01343  0.72
2019 Prigozhin MB, Zhang Y, Schulten K, Gruebele M, Pogorelov TV. Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 30837309 DOI: 10.1073/pnas.1814927116  0.96
2018 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Correction to Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 30480445 DOI: 10.1021/acs.jctc.8b01075  1
2018 Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM. Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Molecular Cell. PMID 30122535 DOI: 10.1016/j.molcel.2018.07.014  0.72
2018 Hadden JA, Perilla JR, Schlicksup CJ, Venkatakrishnan B, Zlotnick A, Schulten K. All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits. Elife. 7. PMID 29708495 DOI: 10.7554/eLife.32478  0.84
2018 Ma W, Whitley KD, Chemla YR, Luthey-Schulten Z, Schulten K. Free energy simulations reveal molecular mechanism for functional switch of a DNA helicase. Elife. 7. PMID 29664402 DOI: 10.7554/eLife.34186  0.72
2018 Milles LF, Schulten K, Gaub HE, Bernardi RC. Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science (New York, N.Y.). 359: 1527-1533. PMID 29599244 DOI: 10.1126/science.aar2094  0.6
2018 Melo MCR, Bernardi RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GB, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z. NAMD goes quantum: an integrative suite for hybrid simulations. Nature Methods. PMID 29578535 DOI: 10.1038/nmeth.4638  0.68
2018 Scheurer M, Rodenkirch P, Siggel M, Bernardi RC, Schulten K, Tajkhorshid E, Rudack T. PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations. Biophysical Journal. 114: 577-583. PMID 29414703 DOI: 10.1016/j.bpj.2017.12.003  0.72
2017 Qiu H, Sarathy A, Schulten K, Leburton JP. Detection and Mapping of DNA Methylation with 2D Material Nanopores. Npj 2d Materials and Applications. 1. PMID 29399640 DOI: 10.1038/s41699-017-0005-7  0.36
2017 Wang M, Quinn CM, Perilla JR, Zhang H, Shirra R, Hou G, Byeon IJ, Suiter CL, Ablan S, Urano E, Nitz TJ, Aiken C, Freed EO, Zhang P, Schulten K, et al. Quenching protein dynamics interferes with HIV capsid maturation. Nature Communications. 8: 1779. PMID 29176596 DOI: 10.1038/s41467-017-01856-y  0.44
2017 Radak BK, Chipot C, Suh D, Jo S, Jiang W, Phillips JC, Schulten K, Roux B. Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 29111720 DOI: 10.1021/acs.jctc.7b00875  1
2017 Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P. CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. Science Advances. 3: e1701264. PMID 28929138 DOI: 10.1126/sciadv.1701264  0.44
2017 Shim J, Banerjee S, Qiu H, Smithe KKH, Estrada D, Bello J, Pop E, Schulten K, Bashir R. Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale. PMID 28795735 DOI: 10.1039/c7nr03092d  0.36
2017 Perilla JR, Schulten K. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nature Communications. 8: 15959. PMID 28722007 DOI: 10.1038/ncomms15959  0.4
2017 Seppälä J, Bernardi RC, Haataja TJK, Hellman M, Pentikäinen OT, Schulten K, Permi P, Ylänne J, Pentikäinen U. Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing. Scientific Reports. 7: 4218. PMID 28652603 DOI: 10.1038/s41598-017-04441-x  0.48
2017 Lippert LG, Dadosh T, Hadden JA, Karnawat V, Diroll BT, Murray CB, Holzbaur ELF, Schulten K, Reck-Peterson SL, Goldman YE. Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk. Proceedings of the National Academy of Sciences of the United States of America. PMID 28533393 DOI: 10.1073/pnas.1620149114  0.84
2017 Comer J, Schulten KJ, Chipot C. Permeability of a fluid lipid bilayer to short-chain alcohols from first principles. Journal of Chemical Theory and Computation. PMID 28475319 DOI: 10.1021/acs.jctc.7b00264  0.68
2017 MacGregor-Chatwin C, Sener M, Barnett SF, Hitchcock A, Barnhart-Dailey MC, Maghlaoui K, Barber J, Timlin JA, Schulten K, Hunter CN. Lateral segregation of photosystem I in cyanobacterial thylakoids. The Plant Cell. PMID 28364021 DOI: 10.1105/tpc.17.00071  0.72
2017 Maji S, Shahoei R, Schulten K, Frank J. Quantitative Characterization of Domain Motions in Molecular Machines. The Journal of Physical Chemistry. B. PMID 28199113 DOI: 10.1021/acs.jpcb.6b10732  0.84
2017 Wehmer M, Rudack T, Beck F, Aufderheide A, Pfeifer G, Plitzko JM, Förster F, Schulten K, Baumeister W, Sakata E. Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Proceedings of the National Academy of Sciences of the United States of America. PMID 28115689 DOI: 10.1073/pnas.1621129114  0.64
2017 Poosarla VG, Li T, Goh BC, Schulten K, Wood TK, Maranas CD. Computational de novo design of antibodies binding to a peptide with high affinity. Biotechnology and Bioengineering. PMID 28059445 DOI: 10.1002/bit.26244  0.48
2016 Stone JE, Hynninen AP, Phillips JC, Schulten K. Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. High Performance Computing : 31st International Conference, Isc High Performance 2016, Frankfurt, Germany, June 19-23, 2016, Proceedings. Isc High Performance (Conference) (31st : 2016 : Frankfurt, Germany). 9945: 188-206. PMID 29202130 DOI: 10.1007/978-3-319-46079-6_14  0.68
2016 Qi Y, Lee J, Singharoy A, Mcgreevy R, Schulten K, Im W. CHRAMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments. The Journal of Physical Chemistry. B. PMID 27936734 DOI: 10.1021/acs.jpcb.6b10568  0.8
2016 Singharoy A, Chipot C, Moradi M, Schulten K. Chemomechanical coupling in hexameric protein-protein interfaces harness energy within V-type ATPases. Journal of the American Chemical Society. PMID 27936329 DOI: 10.1021/jacs.6b10744  0.8
2016 Bozzi AT, Bane LB, Weihofen WA, Singharoy A, Guillen ER, Ploegh HL, Schulten K, Gaudet R. Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter. Structure (London, England : 1993). PMID 27839948 DOI: 10.1016/j.str.2016.09.017  0.8
2016 Stone JE, Sherman WR, Schulten K. Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum : [Proceedings]. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum. 2016: 1048-1057. PMID 27747138 DOI: 10.1109/IPDPSW.2016.121  0.6
2016 Stone JE, Messmer P, Sisneros R, Schulten K. High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum : [Proceedings]. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum. 2016: 1014-1023. PMID 27747137 DOI: 10.1109/IPDPSW.2016.127  0.6
2016 Zhang H, Hou G, Lu M, Ahn J, Byeon IL, Langmead CJ, Perilla JR, Hung I, Gor'kov PL, Gan Z, Brey WW, Case DA, Schulten K, Gronenborn AM, Polenova T. HIV-1 Capsid Function is Regulated by Dynamics: Quantitative Atomic-Resolution Insights by Integrating Magic-Angle-Spinning NMR, QM/MM, and MD. Journal of the American Chemical Society. PMID 27701859 DOI: 10.1021/jacs.6b08744  0.44
2016 Zhang Y, Vuković L, Rudack T, Han W, Schulten K. Correction to "Recognition of Poly-Ubiquitins by the Proteasome through Protein Refolding Guided by Electrostatic and Hydrophobic Interactions". The Journal of Physical Chemistry. B. PMID 27681365 DOI: 10.1021/acs.jpcb.6b09316  1
2016 Barragan AM, Schulten K, Solov'yov IA. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc1 Complex. The Journal of Physical Chemistry. B. PMID 27661199 DOI: 10.1021/acs.jpcb.6b07394  0.48
2016 Bozzi AT, Bane LB, Weihofen WA, McCabe AL, Singharoy A, Chipot CJ, Schulten K, Gaudet R. Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters. Proceedings of the National Academy of Sciences of the United States of America. PMID 27573840 DOI: 10.1073/pnas.1607734113  0.8
2016 Sener M, Strumpfer J, Singharoy A, Hunter CN, Schulten K. Overall energy conversion efficiency of a photosynthetic vesicle. Elife. 5. PMID 27564854 DOI: 10.7554/eLife.09541  0.8
2016 Stone JE, Hallock MJ, Phillips JC, Peterson JR, Luthey-Schulten Z, Schulten K. Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum : [Proceedings]. Ieee International Symposium On Parallel & Distributed Processing, Workshops and Phd Forum. 2016: 89-100. PMID 27516922 DOI: 10.1109/IPDPSW.2016.130  0.68
2016 Thieker DF, Hadden JA, Schulten K, Woods RJ. 3D Implementation of the Symbol Nomenclature for Graphical Representation of Glycans. Glycobiology. PMID 27514939 DOI: 10.1093/glycob/cww076  0.84
2016 Singharoy A, Barragan AM, Thangapandian S, Tajkhorshid E, Schulten K. Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2. Journal of the American Chemical Society. PMID 27508459 DOI: 10.1021/jacs.6b01193  0.8
2016 Tong J, Wu Z, Briggs MM, Schulten K, McIntosh TJ. The Water Permeability and Pore Entrance Structure of Aquaporin-4 Depend on Lipid Bilayer Thickness. Biophysical Journal. 111: 90-99. PMID 27410737 DOI: 10.1016/j.bpj.2016.05.039  0.6
2016 Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K. Molecular dynamics-based renement and validation with Resolution Exchange MDFF for sub-5 Å cryo-electron microscopy maps. Elife. 5. PMID 27383269 DOI: 10.7554/eLife.16105  1
2016 Schweitzer A, Aufderheide A, Rudack T, Beck F, Pfeifer G, Plitzko JM, Sakata E, Schulten K, Förster F, Baumeister W. Structure of the human 26S proteasome at a resolution of 3.9 Å. Proceedings of the National Academy of Sciences of the United States of America. PMID 27342858 DOI: 10.1073/pnas.1608050113  0.64
2016 Goh BC, Wu H, Rynkiewicz MJ, Schulten K, Seaton BA, McCormack FX. Elucidation of Lipid Binding Sites on Lung Surfactant Protein A Using X-ray Crystallography, Mutagenesis, and Molecular Dynamics Simulations. Biochemistry. PMID 27324153 DOI: 10.1021/acs.biochem.6b00048  1
2016 Stone JE, Sener M, Vandivort KL, Barragan A, Singharoy A, Teo I, Ribeiro JV, Isralewitz B, Liu B, Goh BC, Phillips JC, MacGregor-Chatwin C, Johnson MP, Kourkoutis LF, Hunter CN, ... Schulten K, et al. Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing. Parallel Computing. 55: 17-27. PMID 27274603 DOI: 10.1016/j.parco.2015.10.015  1
2016 Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K. QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts. Scientific Reports. 6: 26536. PMID 27216779 DOI: 10.1038/srep26536  1
2016 Poudel KR, Dong Y, Yu H, Su A, Ho T, Liu Y, Schulten K, Bai J. A time-course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Molecular Biology of the Cell. PMID 27170174 DOI: 10.1091/mbc.E16-04-0264  0.96
2016 Teo I, Mayne CG, Schulten K, Lelièvre T. Adaptive multilevel splitting method for molecular dynamics calculation of benzamidine-trypsin dissociation time. Journal of Chemical Theory and Computation. PMID 27159059 DOI: 10.1021/acs.jctc.6b00277  0.8
2016 Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annual Review of Biophysics. PMID 27145875 DOI: 10.1146/annurev-biophys-062215-011113  0.84
2016 Perilla JR, Hadden JA, Goh BC, Mayne CG, Schulten K. All-Atom Molecular Dynamics of Virus Capsids as Drug Targets. The Journal of Physical Chemistry Letters. PMID 27128262 DOI: 10.1021/acs.jpclett.6b00517  0.84
2016 Zhang Y, Schulten K, Gruebele M, Bansal PS, Wilson D, Daly NL. Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide. Biophysical Journal. 110: 1744-1752. PMID 27119635 DOI: 10.1016/j.bpj.2016.03.027  0.36
2016 Heyrana KJ, Goh BC, Perilla JR, Nguyen TN, England MR, Bewley MC, Schulten K, Craven RC. Contributions of charged residues in structurally dynamic capsid surface loops to Rous sarcoma virus assembly. Journal of Virology. PMID 27053549 DOI: 10.1128/JVI.00378-16  1
2016 Liu Y, Singharoy A, Mayne CG, Sengupta A, Raghavachari K, Schulten K, Flood AH. Flexibility Coexists with Shape-persistence in Cyanostar Macrocycles. Journal of the American Chemical Society. PMID 27014837 DOI: 10.1021/jacs.6b00712  1
2016 Zhang Y, Vukovic L, Rudack T, Han W, Schulten K. Recognition of Poly-ubiquitins by the Proteasome through Protein Re-folding Guided by Electrostatic and Hydrophobic Interactions. The Journal of Physical Chemistry. B. PMID 27012670 DOI: 10.1021/acs.jpcb.6b01327  1
2016 Hardy DJ, Wolff MA, Xia J, Schulten K, Skeel RD. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations. The Journal of Chemical Physics. 144: 114112. PMID 27004867 DOI: 10.1063/1.4943868  1
2016 Qiu H, Girdhar A, Schulten K, Leburton JP. Electrically Tunable Quenching of DNA Fluctuations in Biased Solid-State Nanopores. Acs Nano. PMID 26998639 DOI: 10.1021/acsnano.6b00226  1
2016 Liu C, Perilla JR, Ning J, Lu M, Hou G, Ramalho R, Himes BA, Zhao G, Bedwell GJ, Byeon IJ, Ahn J, Gronenborn AM, Prevelige PE, Rousso I, Aiken C, ... ... Schulten K, et al. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site. Nature Communications. 7: 10714. PMID 26940118 DOI: 10.1038/ncomms10714  0.44
2016 Vukovic L, Chipot C, Makino DL, Conti E, Schulten K. Molecular mechanism of processive 3' to 5' RNA translocation in the active subunit of the RNA exosome complex. Journal of the American Chemical Society. PMID 26928279 DOI: 10.1021/jacs.5b12065  1
2016 McGreevy R, Teo I, Singharoy A, Schulten K. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods (San Diego, Calif.). PMID 26804562 DOI: 10.1016/j.ymeth.2016.01.009  1
2016 Gupta P, Liu B, Klepacki D, Gupta V, Schulten K, Mankin AS, Vázquez-Laslop N. Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Nature Chemical Biology. PMID 26727240 DOI: 10.1038/nchembio.1998  0.32
2015 Yu H, Han W, Ma W, Schulten K. Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation. The Journal of Chemical Physics. 143: 243142. PMID 26723627 DOI: 10.1063/1.4936910  1
2015 Cassidy CK, Himes BA, Alvarez FJ, Ma J, Zhao G, Perilla JR, Schulten K, Zhang P. CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. Elife. 4. PMID 26583751 DOI: 10.7554/eLife.08419  1
2015 Qiu H, Sarathy A, Leburton JP, Schulten K. Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores. Nano Letters. PMID 26581231 DOI: 10.1021/acs.nanolett.5b03963  1
2015 Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IL, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, et al. Dynamic allostery governs cyclophilin A-HIV capsid interplay. Proceedings of the National Academy of Sciences of the United States of America. PMID 26553990 DOI: 10.1073/pnas.1516920112  1
2015 Shen R, Han W, Fiorin G, Islam SM, Schulten K, Roux B. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. Plos Computational Biology. 11: e1004368. PMID 26505197 DOI: 10.1371/journal.pcbi.1004368  1
2015 Misra SK, Ghoshal G, Gartia MR, Wu Z, De AK, Ye M, Bromfield CR, Williams EM, Singh K, Tangella KV, Rund L, Schulten K, Schook LB, Ray PS, Burdette EC, et al. Trimodal Therapy: Combining Hyperthermia with Repurposed Bexarotene and Ultrasound for Treating Liver Cancer. Acs Nano. PMID 26435333 DOI: 10.1021/acsnano.5b05974  1
2015 Schoeler C, Bernardi RC, Malinowska KH, Durner E, Ott W, Bayer EA, Schulten K, Nash MA, Gaub HE. Mapping Mechanical Force Propagation through Biomolecular Complexes. Nano Letters. 15: 7370-6. PMID 26259544 DOI: 10.1021/acs.nanolett.5b02727  1
2015 Wang X, Vukovic L, Koh HR, Schulten K, Myong S. Dynamic profiling of double-stranded RNA binding proteins. Nucleic Acids Research. 43: 7566-76. PMID 26184879 DOI: 10.1093/nar/gkv726  1
2015 Singharoy A, Venkatakrishnan B, Liu Y, Mayne CG, Lee S, Chen CH, Zlotnick A, Schulten K, Flood AH. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles. Journal of the American Chemical Society. 137: 8810-8. PMID 26121416 DOI: 10.1021/jacs.5b04407  0.96
2015 Goh BC, Perilla JR, England MR, Heyrana KJ, Craven RC, Schulten K. Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis. Structure (London, England : 1993). PMID 26118533 DOI: 10.1016/j.str.2015.05.017  1
2015 Lesieur C, Schulten K. Editorial overview: Theory and simulation. Current Opinion in Structural Biology. 31: v-vi. PMID 26055121 DOI: 10.1016/j.sbi.2015.05.008  1
2015 Landry MP, Vukovi? L, Kruss S, Bisker G, Landry AM, Islam S, Jain R, Schulten K, Strano MS. Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 119: 10048-10058. PMID 26005509 DOI: 10.1021/jp511448e  1
2015 Wirth AJ, Liu Y, Prigozhin MB, Schulten K, Gruebele M. Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations. Journal of the American Chemical Society. 137: 7152-9. PMID 25988868 DOI: 10.1021/jacs.5b02474  1
2015 Englander MT, Avins JL, Fleisher RC, Liu B, Effraim PR, Wang J, Schulten K, Leyh TS, Gonzalez RL, Cornish VW. The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center. Proceedings of the National Academy of Sciences of the United States of America. 112: 6038-43. PMID 25918365 DOI: 10.1073/pnas.1424712112  1
2015 Perilla JR, Goh BC, Cassidy CK, Liu B, Bernardi RC, Rudack T, Yu H, Wu Z, Schulten K. Molecular dynamics simulations of large macromolecular complexes. Current Opinion in Structural Biology. 31: 64-74. PMID 25845770 DOI: 10.1016/j.sbi.2015.03.007  1
2015 Girdhar A, Sathe C, Schulten K, Leburton JP. Tunable graphene quantum point contact transistor for DNA detection and characterization. Nanotechnology. 26: 134005. PMID 25765702 DOI: 10.1088/0957-4484/26/13/134005  1
2015 Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K. Multilevel Summation Method for Electrostatic Force Evaluation. Journal of Chemical Theory and Computation. 11: 766-779. PMID 25691833 DOI: 10.1021/ct5009075  1
2015 Ma W, Schulten K. Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. Journal of the American Chemical Society. 137: 3031-40. PMID 25646698 DOI: 10.1021/ja512605w  1
2015 Bernardi RC, Melo MC, Schulten K. Enhanced sampling techniques in molecular dynamics simulations of biological systems. Biochimica Et Biophysica Acta. 1850: 872-877. PMID 25450171 DOI: 10.1016/j.bbagen.2014.10.019  1
2015 Fraiberg M, Afanzar O, Cassidy CK, Gabashvili A, Schulten K, Levin Y, Eisenbach M. CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli. Molecular Microbiology. 95: 231-44. PMID 25388160 DOI: 10.1111/mmi.12858  1
2015 Barragan AM, Crofts AR, Schulten K, Solov'yov IA. Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. The Journal of Physical Chemistry. B. 119: 433-47. PMID 25372183 DOI: 10.1021/jp510022w  1
2015 Yu H, Han W, Ma W, Schulten K. Transient β -hairpin formation in α -synuclein monomer revealed by coarse-grained molecular dynamics simulation Journal of Chemical Physics. 143. DOI: 10.1063/1.4936910  1
2015 Stone JE, Sener M, Vandivort KL, Barragan A, Singharoy A, Teo I, Ribeiro JV, Isralewitz B, Liu B, Goh BC, Phillips JC, MacGregor-Chatwin C, Johnson MP, Kourkoutis LF, Hunter CN, ... Schulten K, et al. Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing Parallel Computing. DOI: 10.1016/j.parco.2015.10.015  1
2014 Comer J, Schulten K, Chipot C. Diffusive Models of Membrane Permeation with Explicit Orientational Freedom. Journal of Chemical Theory and Computation. 10: 2710-8. PMID 26586505 DOI: 10.1021/ct500209j  0.68
2014 Comer J, Phillips JC, Schulten K, Chipot C. Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules. Journal of Chemical Theory and Computation. 10: 5276-85. PMID 26583211 DOI: 10.1021/ct500874p  0.68
2014 Comer J, Schulten K, Chipot C. Calculation of Lipid-Bilayer Permeabilities Using an Average Force. Journal of Chemical Theory and Computation. 10: 554-64. PMID 26580032 DOI: 10.1021/ct400925s  0.68
2014 Aghtar M, Strümpfer J, Olbrich C, Schulten K, Kleinekathöfer U. Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems. The Journal of Physical Chemistry Letters. 5: 3131-7. PMID 26276324 DOI: 10.1021/jz501351p  0.84
2014 Schoeler C, Malinowska KH, Bernardi RC, Milles LF, Jobst MA, Durner E, Ott W, Fried DB, Bayer EA, Schulten K, Gaub HE, Nash MA. Ultrastable cellulosome-adhesion complex tightens under load. Nature Communications. 5: 5635. PMID 25482395 DOI: 10.1038/ncomms6635  1
2014 Blanchard AE, Arcario MJ, Schulten K, Tajkhorshid E. A highly tilted membrane configuration for the prefusion state of synaptobrevin. Biophysical Journal. 107: 2112-21. PMID 25418096 DOI: 10.1016/j.bpj.2014.09.013  1
2014 Girdhar A, Sathe C, Schulten K, Leburton JP. Gate-Modulated Graphene Quantum Point Contact Device for DNA Sensing. Journal of Computational Electronics. 13: 839-846. PMID 25386110 DOI: 10.1007/s10825-014-0596-6  1
2014 Stone JE, McGreevy R, Isralewitz B, Schulten K. GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting. Faraday Discussions. 169: 265-83. PMID 25340325 DOI: 10.1039/c4fd00005f  1
2014 Sathe C, Girdhar A, Leburton JP, Schulten K. Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores. Nanotechnology. 25: 445105. PMID 25325530 DOI: 10.1088/0957-4484/25/44/445105  1
2014 Cai E, Ge P, Lee SH, Jeyifous O, Wang Y, Liu Y, Wilson KM, Lim SJ, Baird MA, Stone JE, Lee KY, Davidson MW, Chung HJ, Schulten K, Smith AM, et al. Stable small quantum dots for synaptic receptor tracking on live neurons. Angewandte Chemie (International Ed. in English). 53: 12484-8. PMID 25255882 DOI: 10.1002/anie.201405735  1
2014 McGreevy R, Singharoy A, Li Q, Zhang J, Xu D, Perozo E, Schulten K. xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures. Acta Crystallographica. Section D, Biological Crystallography. 70: 2344-55. PMID 25195748 DOI: 10.1107/S1399004714013856  1
2014 Wu Z, Schulten K. Synaptotagmin's role in neurotransmitter release likely involves Ca(2+)-induced conformational transition. Biophysical Journal. 107: 1156-66. PMID 25185551 DOI: 10.1016/j.bpj.2014.07.041  1
2014 Han W, Schulten K. Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations. Journal of the American Chemical Society. 136: 12450-60. PMID 25134066 DOI: 10.1021/ja507002p  1
2014 Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R. A structural model of the active ribosome-bound membrane protein insertase YidC. Elife. 3: e03035. PMID 25012291 DOI: 10.7554/eLife.03035  1
2014 Bernardi RC, Cann I, Schulten K. Molecular dynamics study of enhanced Man5B enzymatic activity. Biotechnology For Biofuels. 7: 83. PMID 24976862 DOI: 10.1186/1754-6834-7-83  1
2014 Sothiselvam S, Liu B, Han W, Ramu H, Klepacki D, Atkinson GC, Brauer A, Remm M, Tenson T, Schulten K, Vázquez-Laslop N, Mankin AS. Macrolide antibiotics allosterically predispose the ribosome for translation arrest. Proceedings of the National Academy of Sciences of the United States of America. 111: 9804-9. PMID 24961372 DOI: 10.1073/pnas.1403586111  1
2014 Jiang W, Phillips JC, Huang L, Fajer M, Meng Y, Gumbart JC, Luo Y, Schulten K, Roux B. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD. Computer Physics Communications. 185: 908-916. PMID 24944348 DOI: 10.1016/j.cpc.2013.12.014  1
2014 Chandler DE, Strümpfer J, Sener M, Scheuring S, Schulten K. Light harvesting by lamellar chromatophores in Rhodospirillum photometricum. Biophysical Journal. 106: 2503-10. PMID 24896130 DOI: 10.1016/j.bpj.2014.04.030  1
2014 Vukovi? L, Koh HR, Myong S, Schulten K. Substrate recognition and specificity of double-stranded RNA binding proteins. Biochemistry. 53: 3457-66. PMID 24801449 DOI: 10.1021/bi500352s  1
2014 Zhou Q, Li J, Yu H, Zhai Y, Gao Z, Liu Y, Pang X, Zhang L, Schulten K, Sun F, Chen C. Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα. Nature Communications. 5: 3552. PMID 24675427 DOI: 10.1038/ncomms4552  1
2014 Gamini R, Han W, Stone JE, Schulten K. Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating. Plos Computational Biology. 10: e1003488. PMID 24626154 DOI: 10.1371/journal.pcbi.1003488  1
2014 Qi Y, Cheng X, Han W, Jo S, Schulten K, Im W. CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations. Journal of Chemical Information and Modeling. 54: 1003-9. PMID 24624945 DOI: 10.1021/ci500007n  1
2014 Wang Y, Liu Y, Deberg HA, Nomura T, Hoffman MT, Rohde PR, Schulten K, Martinac B, Selvin PR. Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel. Elife. 3: e01834. PMID 24550255 DOI: 10.7554/eLife.01834  1
2014 Cartron ML, Olsen JD, Sener M, Jackson PJ, Brindley AA, Qian P, Dickman MJ, Leggett GJ, Schulten K, Neil Hunter C. Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides. Biochimica Et Biophysica Acta. 1837: 1769-80. PMID 24530865 DOI: 10.1016/j.bbabio.2014.02.003  1
2014 Li Q, Wanderling S, Paduch M, Medovoy D, Singharoy A, McGreevy R, Villalba-Galea CA, Hulse RE, Roux B, Schulten K, Kossiakoff A, Perozo E. Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain. Nature Structural & Molecular Biology. 21: 244-52. PMID 24487958 DOI: 10.1038/nsmb.2768  1
2014 Solov'yov IA, Domratcheva T, Schulten K. Separation of photo-induced radical pair in cryptochrome to a functionally critical distance. Scientific Reports. 4: 3845. PMID 24457842 DOI: 10.1038/srep03845  1
2014 Liu Y, Prigozhin MB, Schulten K, Gruebele M. Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment. Journal of the American Chemical Society. 136: 4265-72. PMID 24437525 DOI: 10.1021/ja412639u  1
2014 Stone JE, Isralewitz B, Schulten K. Early experiences scaling VMD molecular visualization and analysis jobs on blue waters Proceedings - 2013 Extreme Scaling Workshop, Xsw 2013. 43-50. DOI: 10.1109/XSW.2013.10  1
2014 Phillips JC, Stone JE, Vandivort KL, Armstrong TG, Wozniak JM, Wilde M, Schulten K. Petascale Tcl with NAMD, VMD, and Swift/T Proceedings of Hptcdl 2014: 1st Workshop For High Performance Technical Computing in Dynamic Languages - Held in Conjunction With Sc 2014: the International Conference For High Performance Computing, Networking, Storage and Analysis. 6-17. DOI: 10.1109/HPTCDL.2014.7  1
2014 Comer J, Phillips JC, Schulten K, Chipot C. Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules Journal of Chemical Theory and Computation. 10: 5276-5285. DOI: 10.1021/ct500874p  1
2014 Comer J, Schulten K, Chipot C. Diffusive models of membrane permeation with explicit orientational freedom Journal of Chemical Theory and Computation. 10: 2710-2718. DOI: 10.1021/ct500209j  1
2014 Comer J, Schulten K, Chipot C. Calculation of lipid-bilayer permeabilities using an average force Journal of Chemical Theory and Computation. 10: 554-564. DOI: 10.1021/ct400925s  1
2014 Schulten K, Hayashi S. Quantum biology of retinal Quantum Effects in Biology. 237-263. DOI: 10.1017/CBO9780511863189.013  1
2014 Solov'yov IA, Ritz T, Schulten K, Hore PJ. A chemical compass for bird navigation Quantum Effects in Biology. 218-236. DOI: 10.1017/CBO9780511863189.012  1
2014 Kosztin I, Schulten K. Structure, function, and quantum dynamics of pigment–protein complexes Quantum Effects in Biology. 123-143. DOI: 10.1017/CBO9780511863189.007  1
2013 Goh BC, Rynkiewicz MJ, Cafarella TR, White MR, Hartshorn KL, Allen K, Crouch EC, Calin O, Seeberger PH, Schulten K, Seaton BA. Molecular mechanisms of inhibition of influenza by surfactant protein D revealed by large-scale molecular dynamics simulation. Biochemistry. 52: 8527-38. PMID 24224757 DOI: 10.1021/bi4010683  1
2013 Teo I, Schulten K. A computational kinetic model of diffusion for molecular systems. The Journal of Chemical Physics. 139: 121929. PMID 24089741 DOI: 10.1063/1.4820876  1
2013 Girdhar A, Sathe C, Schulten K, Leburton JP. Graphene quantum point contact transistor for DNA sensing. Proceedings of the National Academy of Sciences of the United States of America. 110: 16748-53. PMID 24082108 DOI: 10.1073/pnas.1308885110  1
2013 Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC. Rapid parameterization of small molecules using the Force Field Toolkit. Journal of Computational Chemistry. 34: 2757-70. PMID 24000174 DOI: 10.1002/jcc.23422  1
2013 Han W, Schulten K. Characterization of folding mechanisms of Trp-cage and WW-domain by network analysis of simulations with a hybrid-resolution model. The Journal of Physical Chemistry. B. 117: 13367-77. PMID 23915394 DOI: 10.1021/jp404331d  1
2013 Zhao G, Perilla JR, Yufenyuy EL, Meng X, Chen B, Ning J, Ahn J, Gronenborn AM, Schulten K, Aiken C, Zhang P. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 497: 643-6. PMID 23719463 DOI: 10.1038/nature12162  1
2013 Zhang K, Wang L, Liu Y, Chan KY, Pang X, Schulten K, Dong Z, Sun F. Flexible interwoven termini determine the thermal stability of thermosomes. Protein & Cell. 4: 432-44. PMID 23709365 DOI: 10.1007/s13238-013-3026-9  1
2013 Aghtar M, Strümpfer J, Olbrich C, Schulten K, Kleinekathöfer U. The FMO complex in a glycerol-water mixture. The Journal of Physical Chemistry. B. 117: 7157-63. PMID 23697741 DOI: 10.1021/jp311380k  1
2013 Prigozhin MB, Liu Y, Wirth AJ, Kapoor S, Winter R, Schulten K, Gruebele M. Misplaced helix slows down ultrafast pressure-jump protein folding. Proceedings of the National Academy of Sciences of the United States of America. 110: 8087-92. PMID 23620522 DOI: 10.1073/pnas.1219163110  1
2013 Shim J, Humphreys GI, Venkatesan BM, Munz JM, Zou X, Sathe C, Schulten K, Kosari F, Nardulli AM, Vasmatzis G, Bashir R. Detection and quantification of methylation in DNA using solid-state nanopores. Scientific Reports. 3: 1389. PMID 23474808 DOI: 10.1038/srep01389  1
2013 Freddolino PL, Gardner KH, Schulten K. Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 12: 1158-70. PMID 23407663 DOI: 10.1039/c3pp25400c  1
2013 Li W, Atkinson GC, Thakor NS, Allas U, Lu CC, Chan KY, Tenson T, Schulten K, Wilson KS, Hauryliuk V, Frank J. Mechanism of tetracycline resistance by ribosomal protection protein Tet(O). Nature Communications. 4: 1477. PMID 23403578 DOI: 10.1038/ncomms2470  1
2013 Crofts AR, Hong S, Wilson C, Burton R, Victoria D, Harrison C, Schulten K. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. Biochimica Et Biophysica Acta. 1827: 1362-77. PMID 23396004 DOI: 10.1016/j.bbabio.2013.01.009  1
2013 Yu H, Schulten K. Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. Plos Computational Biology. 9: e1002892. PMID 23382665 DOI: 10.1371/journal.pcbi.1002892  1
2013 Wang X, Xu F, Liu J, Gao B, Liu Y, Zhai Y, Ma J, Zhang K, Baker TS, Schulten K, Zheng D, Pang H, Sun F. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography. Plos Pathogens. 9: e1003132. PMID 23341770 DOI: 10.1371/journal.ppat.1003132  1
2013 Severin PM, Zou X, Schulten K, Gaub HE. Effects of cytosine hydroxymethylation on DNA strand separation. Biophysical Journal. 104: 208-15. PMID 23332073 DOI: 10.1016/j.bpj.2012.11.013  1
2013 Lai Y, Diao J, Liu Y, Ishitsuka Y, Su Z, Schulten K, Ha T, Shin YK. Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1. Proceedings of the National Academy of Sciences of the United States of America. 110: 1333-8. PMID 23300284 DOI: 10.1073/pnas.1218818110  1
2013 Gumbart JC, Teo I, Roux B, Schulten K. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. Journal of the American Chemical Society. 135: 2291-7. PMID 23298280 DOI: 10.1021/ja310777k  1
2013 Landry MP, Zou X, Wang L, Huang WM, Schulten K, Chemla YR. DNA target sequence identification mechanism for dimer-active protein complexes. Nucleic Acids Research. 41: 2416-27. PMID 23275566 DOI: 10.1093/nar/gks1345  1
2013 Stone JE, Vandivort KL, Schulten K. GPU-accelerated molecular visualization on petascale supercomputing platforms Proc. of Ultravis 2013: 8th Int. Workshop On Ultrascale Visualization - Held in Conjunction With Sc 2013: the Int. Conference For High Performance Computing, Networking, Storage and Analysis. DOI: 10.1145/2535571.2535595  1
2012 Harrison CB, Schulten K. Quantum and classical dynamics simulations of ATP hydrolysis in solution. Journal of Chemical Theory and Computation. 8: 2328-2335. PMID 23293550 DOI: 10.1021/ct200886j  1
2012 Han W, Schulten K. Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. Journal of Chemical Theory and Computation. 8: 4413-4424. PMID 23204949 DOI: 10.1021/ct300696c  1
2012 Vargas E, Yarov-Yarovoy V, Khalili-Araghi F, Catterall WA, Klein ML, Tarek M, Lindahl E, Schulten K, Perozo E, Bezanilla F, Roux B. An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations. The Journal of General Physiology. 140: 587-94. PMID 23183694 DOI: 10.1085/jgp.201210873  1
2012 Strümpfer J, Schulten K. Open Quantum Dynamics Calculations with the Hierarchy Equations of Motion on Parallel Computers. Journal of Chemical Theory and Computation. 8: 2808-2816. PMID 23105920 DOI: 10.1021/ct3003833  1
2012 Tanner DE, Phillips JC, Schulten K. GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations. Journal of Chemical Theory and Computation. 8: 2521-2530. PMID 23049488 DOI: 10.1021/ct3003089  1
2012 Chandler DE, Penin F, Schulten K, Chipot C. The p7 protein of hepatitis C virus forms structurally plastic, minimalist ion channels. Plos Computational Biology. 8: e1002702. PMID 23028296 DOI: 10.1371/journal.pcbi.1002702  1
2012 Solov'yov IA, Domratcheva T, Moughal Shahi AR, Schulten K. Decrypting cryptochrome: revealing the molecular identity of the photoactivation reaction. Journal of the American Chemical Society. 134: 18046-52. PMID 23009093 DOI: 10.1021/ja3074819  1
2012 Vergara-Jaque A, Poblete H, Lee EH, Schulten K, González-Nilo F, Chipot C. Molecular basis of drug resistance in A/H1N1 virus. Journal of Chemical Information and Modeling. 52: 2650-6. PMID 22978683 DOI: 10.1021/ci300343w  1
2012 Solov'yov IA, Chang PY, Schulten K. Vibrationally assisted electron transfer mechanism of olfaction: myth or reality? Physical Chemistry Chemical Physics : Pccp. 14: 13861-71. PMID 22899100 DOI: 10.1039/c2cp41436h  1
2012 Chen Y, Cruz-Chu ER, Woodard JC, Gartia MR, Schulten K, Liu L. Electrically induced conformational change of peptides on metallic nanosurfaces. Acs Nano. 6: 8847-56. PMID 22897498 DOI: 10.1021/nn3027408  1
2012 Strümpfer J, Schulten K. Excited state dynamics in photosynthetic reaction center and light harvesting complex 1. The Journal of Chemical Physics. 137: 065101. PMID 22897312 DOI: 10.1063/1.4738953  1
2012 von Castelmur E, Strümpfer J, Franke B, Bogomolovas J, Barbieri S, Qadota H, Konarev PV, Svergun DI, Labeit S, Benian GM, Schulten K, Mayans O. Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase. Proceedings of the National Academy of Sciences of the United States of America. 109: 13608-13. PMID 22869697 DOI: 10.1073/pnas.1200697109  1
2012 Gumbart J, Schreiner E, Wilson DN, Beckmann R, Schulten K. Mechanisms of SecM-mediated stalling in the ribosome. Biophysical Journal. 103: 331-41. PMID 22853911 DOI: 10.1016/j.bpj.2012.06.005  1
2012 Strümpfer J, Sener M, Schulten K. How Quantum Coherence Assists Photosynthetic Light Harvesting. The Journal of Physical Chemistry Letters. 3: 536-542. PMID 22844553 DOI: 10.1021/jz201459c  1
2012 Liu Y, Strümpfer J, Freddolino PL, Gruebele M, Schulten K. Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations. The Journal of Physical Chemistry Letters. 3: 1117-1123. PMID 22737279 DOI: 10.1021/jz300017c  1
2012 Aghtar M, Liebers J, Strümpfer J, Schulten K, Kleinekathöfer U. Juxtaposing density matrix and classical path-based wave packet dynamics. The Journal of Chemical Physics. 136: 214101. PMID 22697524 DOI: 10.1063/1.4723669  1
2012 Chan KY, Trabuco LG, Schreiner E, Schulten K. Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method. Biopolymers. 97: 678-86. PMID 22696404 DOI: 10.1002/bip.22042  1
2012 van Eijk M, Rynkiewicz MJ, White MR, Hartshorn KL, Zou X, Schulten K, Luo D, Crouch EC, Cafarella TR, Head JF, Haagsman HP, Seaton BA. A unique sugar-binding site mediates the distinct anti-influenza activity of pig surfactant protein D. The Journal of Biological Chemistry. 287: 26666-77. PMID 22685299 DOI: 10.1074/jbc.M112.368571  1
2012 Lee W, Strümpfer J, Bennett V, Schulten K, Marszalek PE. Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats. The Journal of Biological Chemistry. 287: 19115-21. PMID 22514283 DOI: 10.1074/jbc.M112.365569  1
2012 Agirrezabala X, Liao HY, Schreiner E, Fu J, Ortiz-Meoz RF, Schulten K, Green R, Frank J. Structural characterization of mRNA-tRNA translocation intermediates. Proceedings of the National Academy of Sciences of the United States of America. 109: 6094-9. PMID 22467828 DOI: 10.1073/pnas.1201288109  1
2012 Khalili-Araghi F, Tajkhorshid E, Roux B, Schulten K. Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains. Biophysical Journal. 102: 258-67. PMID 22339862 DOI: 10.1016/j.bpj.2011.10.057  1
2012 Solov'yov IA, Schulten K. Reaction kinetics and mechanism of magnetic field effects in cryptochrome. The Journal of Physical Chemistry. B. 116: 1089-99. PMID 22171949 DOI: 10.1021/jp209508y  1
2012 Zou X, Ma W, Solov'yov IA, Chipot C, Schulten K. Recognition of methylated DNA through methyl-CpG binding domain proteins. Nucleic Acids Research. 40: 2747-58. PMID 22110028 DOI: 10.1093/nar/gkr1057  1
2012 Lee W, Strümpfer J, Bennett V, Schulten K, Marszalek PE. Mutation of conserved histidines alters tertiary structure and nanomechanics of consensus ankyrin repeats (Journal of Biological Chemistry (2012) 287, (19115-19121) DOI: 10.1074/jbc.A112.365569) Journal of Biological Chemistry. 287: 35539. DOI: 10.1074/jbc.A112.365569  1
2011 Tanner DE, Chan KY, Phillips JC, Schulten K. Parallel Generalized Born Implicit Solvent Calculations with NAMD. Journal of Chemical Theory and Computation. 7: 3635-3642. PMID 22121340 DOI: 10.1021/ct200563j  1
2011 Sathe C, Zou X, Leburton JP, Schulten K. Computational investigation of DNA detection using graphene nanopores. Acs Nano. 5: 8842-51. PMID 21981556 DOI: 10.1021/nn202989w  1
2011 Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure (London, England : 1993). 19: 1211-8. PMID 21893283 DOI: 10.1016/j.str.2011.07.017  1
2011 Olbrich C, Strümpfer J, Schulten K, Kleinekathöfer U. Theory and Simulation of the Environmental Effects on FMO Electronic Transitions. The Journal of Physical Chemistry Letters. 2011: 1771-1776. PMID 21804928 DOI: 10.1021/jz2007676  1
2011 Hsin J, LaPointe LM, Kazy A, Chipot C, Senes A, Schulten K. Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix. Journal of the American Chemical Society. 133: 14071-81. PMID 21790140 DOI: 10.1021/ja204869h  1
2011 Severin PM, Zou X, Gaub HE, Schulten K. Cytosine methylation alters DNA mechanical properties. Nucleic Acids Research. 39: 8740-51. PMID 21775342 DOI: 10.1093/nar/gkr578  1
2011 Gamini R, Sotomayor M, Chipot C, Schulten K. Cytoplasmic domain filter function in the mechanosensitive channel of small conductance. Biophysical Journal. 101: 80-9. PMID 21723817 DOI: 10.1016/j.bpj.2011.05.042  1
2011 Liu Y, Hsin J, Kim H, Selvin PR, Schulten K. Extension of a three-helix bundle domain of myosin VI and key role of calmodulins. Biophysical Journal. 100: 2964-73. PMID 21689530 DOI: 10.1016/j.bpj.2011.05.010  1
2011 Wang Y, Harrison CB, Schulten K, McCammon JA. Implementation of Accelerated Molecular Dynamics in NAMD. Computational Science & Discovery. 4. PMID 21686063 DOI: 10.1088/1749-4699/4/1/015002  0.84
2011 Tanner DE, Ma W, Chen Z, Schulten K. Theoretical and computational investigation of flagellin translocation and bacterial flagellum growth. Biophysical Journal. 100: 2548-56. PMID 21641299 DOI: 10.1016/j.bpj.2011.04.036  1
2011 Olbrich C, Jansen TL, Liebers J, Aghtar M, Strümpfer J, Schulten K, Knoester J, Kleinekathöfer U. From atomistic modeling to excitation transfer and two-dimensional spectra of the FMO light-harvesting complex. The Journal of Physical Chemistry. B. 115: 8609-21. PMID 21635010 DOI: 10.1021/jp202619a  1
2011 Schreiner E, Trabuco LG, Freddolino PL, Schulten K. Stereochemical errors and their implications for molecular dynamics simulations. Bmc Bioinformatics. 12: 190. PMID 21605430 DOI: 10.1186/1471-2105-12-190  1
2011 Jiang W, Hardy DJ, Phillips JC, Mackerell AD, Schulten K, Roux B. High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD. The Journal of Physical Chemistry Letters. 2: 87-92. PMID 21572567 DOI: 10.1021/jz101461d  1
2011 Gumbart J, Chipot C, Schulten K. Free energy of nascent-chain folding in the translocon. Journal of the American Chemical Society. 133: 7602-7. PMID 21524073 DOI: 10.1021/ja2019299  1
2011 Frauenfeld J, Gumbart J, Sluis EO, Funes S, Gartmann M, Beatrix B, Mielke T, Berninghausen O, Becker T, Schulten K, Beckmann R. Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nature Structural & Molecular Biology. 18: 614-21. PMID 21499241 DOI: 10.1038/nsmb.2026  1
2011 Kleinekathöfer U, Isralewitz B, Dittrich M, Schulten K. Domain motion of individual F1-ATPase β-subunits during unbiased molecular dynamics simulations. The Journal of Physical Chemistry. A. 115: 7267-74. PMID 21452901 DOI: 10.1021/jp2005088  1
2011 Strümpfer J, Schulten K. The effect of correlated bath fluctuations on exciton transfer. The Journal of Chemical Physics. 134: 095102. PMID 21385000 DOI: 10.1063/1.3557042  1
2011 Chen W, Lou J, Hsin J, Schulten K, Harvey SC, Zhu C. Molecular dynamics simulations of forced unbending of integrin α(v)β₃. Plos Computational Biology. 7: e1001086. PMID 21379327 DOI: 10.1371/journal.pcbi.1001086  1
2011 Agirrezabala X, Schreiner E, Trabuco LG, Lei J, Ortiz-Meoz RF, Schulten K, Green R, Frank J. Structural insights into cognate versus near-cognate discrimination during decoding. The Embo Journal. 30: 1497-507. PMID 21378755 DOI: 10.1038/emboj.2011.58  1
2011 Li W, Trabuco LG, Schulten K, Frank J. Molecular dynamics of EF-G during translocation. Proteins. 79: 1478-86. PMID 21365677 DOI: 10.1002/prot.22976  1
2011 Åžener M, Strümpfer J, Hsin J, Chandler D, Scheuring S, Hunter CN, Schulten K. Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 518-31. PMID 21344591 DOI: 10.1002/cphc.201000944  1
2011 Kaminski CF, Sackmann E, Schulten K. Theodor Förster: a giant of modern photochemistry. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 12: 423-4. PMID 21344585 DOI: 10.1002/cphc.201100041  1
2011 Hsin J, Strümpfer J, Lee EH, Schulten K. Molecular origin of the hierarchical elasticity of titin: simulation, experiment, and theory. Annual Review of Biophysics. 40: 187-203. PMID 21332356 DOI: 10.1146/annurev-biophys-072110-125325  1
2011 Song SH, Freddolino PL, Nash AI, Carroll EC, Schulten K, Gardner KH, Larsen DS. Modulating LOV domain photodynamics with a residue alteration outside the chromophore binding site. Biochemistry. 50: 2411-23. PMID 21323358 DOI: 10.1021/bi200198x  1
2011 Hsin J, Schulten K. Improved resolution of tertiary structure elasticity in muscle protein. Biophysical Journal. 100: L22-4. PMID 21320420 DOI: 10.1016/j.bpj.2011.01.019  1
2011 Gumbart J, Chipot C, Schulten K. Free-energy cost for translocon-assisted insertion of membrane proteins. Proceedings of the National Academy of Sciences of the United States of America. 108: 3596-601. PMID 21317362 DOI: 10.1073/pnas.1012758108  1
2011 Olbrich C, Strümpfer J, Schulten K, Kleinekathöfer U. Quest for spatially correlated fluctuations in the FMO light-harvesting complex. The Journal of Physical Chemistry. B. 115: 758-64. PMID 21142050 DOI: 10.1021/jp1099514  1
2011 Trabuco LG, Schreiner E, Gumbart J, Hsin J, Villa E, Schulten K. Applications of the molecular dynamics flexible fitting method. Journal of Structural Biology. 173: 420-7. PMID 20932910 DOI: 10.1016/j.jsb.2010.09.024  1
2011 Gumbart J, Schreiner E, Trabuco LG, Chan KY, Schulten K. Viewing the mechanisms of translation through the computational microscope Molecular Machines in Biology: Workshop of the Cell. 142-157. DOI: 10.1017/CBO9781139003704.010  1
2011 Hardy DJ, Stone JE, Vandivort KL, Gohara D, Rodrigues C, Schulten K. Fast molecular electrostatics algorithms on GPUs Gpu Computing Gems Emerald Edition. 43-58. DOI: 10.1016/B978-0-12-384988-5.00004-8  1
2011 Stone JE, Hardy DJ, Saam J, Vandivort KL, Schulten K. GPU-accelerated computation and interactive display of molecular orbitals Gpu Computing Gems Emerald Edition. 5-18. DOI: 10.1016/B978-0-12-384988-5.00001-2  1
2011 Stone JE, Vandivort KL, Schulten K. Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6939: 1-12. DOI: 10.1007/978-3-642-24031-7_1  1
2010 Solov'yov IA, Schulten K, Greiner W. [The Navigation of Birds and Other Animals in the Magnetic Field.] Physik Journal. 9: 23-28. PMID 23378826  0.48
2010 Freddolino PL, Harrison CB, Liu Y, Schulten K. Challenges in protein folding simulations: Timescale, representation, and analysis. Nature Physics. 6: 751-758. PMID 21297873 DOI: 10.1038/nphys1713  1
2010 Hsin J, Strümpfer J, Sener M, Qian P, Hunter CN, Schulten K. Energy Transfer Dynamics in an RC-LH1-PufX Tubular Photosynthetic Membrane. New Journal of Physics. 12. PMID 21152381 DOI: 10.1088/1367-2630/12/8/085005  1
2010 Kim H, Hsin J, Liu Y, Selvin PR, Schulten K. Formation of salt bridges mediates internal dimerization of myosin VI medial tail domain. Structure (London, England : 1993). 18: 1443-9. PMID 21070943 DOI: 10.1016/j.str.2010.09.011  1
2010 Le L, Lee EH, Hardy DJ, Truong TN, Schulten K. Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases. Plos Computational Biology. 6. PMID 20885781 DOI: 10.1371/journal.pcbi.1000939  1
2010 Kijac A, Shih AY, Nieuwkoop AJ, Schulten K, Sligar SG, Rienstra CM. Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance. Biochemistry. 49: 9190-8. PMID 20804175 DOI: 10.1021/bi1013722  1
2010 Zou X, Liu Y, Chen Z, Cárdenas-Jirón GI, Schulten K. Flow-induced beta-hairpin folding of the glycoprotein Ibalpha beta-switch. Biophysical Journal. 99: 1182-91. PMID 20713002 DOI: 10.1016/j.bpj.2010.05.035  1
2010 Roos WH, Gibbons MM, Arkhipov A, Uetrecht C, Watts NR, Wingfield PT, Steven AC, Heck AJ, Schulten K, Klug WS, Wuite GJ. Squeezing protein shells: how continuum elastic models, molecular dynamics simulations, and experiments coalesce at the nanoscale. Biophysical Journal. 99: 1175-81. PMID 20713001 DOI: 10.1016/j.bpj.2010.05.033  1
2010 Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, Schulten K. The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. Journal of Molecular Biology. 402: 741-60. PMID 20691699 DOI: 10.1016/j.jmb.2010.07.056  1
2010 Stone JE, Hardy DJ, Ufimtsev IS, Schulten K. GPU-accelerated molecular modeling coming of age. Journal of Molecular Graphics & Modelling. 29: 116-25. PMID 20675161 DOI: 10.1016/j.jmgm.2010.06.010  1
2010 ?ener M, Strümpfer J, Timney JA, Freiberg A, Hunter CN, Schulten K. Photosynthetic vesicle architecture and constraints on efficient energy harvesting Biophysical Journal. 99: 67-75. PMID 20655834 DOI: 10.1016/j.bpj.2010.04.013  1
2010 Solov'yov IA, Mouritsen H, Schulten K. Acuity of a cryptochrome and vision-based magnetoreception system in birds. Biophysical Journal. 99: 40-9. PMID 20655831 DOI: 10.1016/j.bpj.2010.03.053  1
2010 Cruz-Chu ER, Schulten K. Computational microscopy of the role of protonable surface residues in nanoprecipitation oscillations. Acs Nano. 4: 4463-74. PMID 20597534 DOI: 10.1021/nn100399f  1
2010 Saam J, Rosini E, Molla G, Schulten K, Pollegioni L, Ghisla S. O2 reactivity of flavoproteins: dynamic access of dioxygen to the active site and role of a H+ relay system in D-amino acid oxidase. The Journal of Biological Chemistry. 285: 24439-46. PMID 20498362 DOI: 10.1074/jbc.M110.131193  1
2010 Khalili-Araghi F, Jogini V, Yarov-Yarovoy V, Tajkhorshid E, Roux B, Schulten K. Calculation of the gating charge for the Kv1.2 voltage-activated potassium channel. Biophysical Journal. 98: 2189-98. PMID 20483327 DOI: 10.1016/j.bpj.2010.02.056  1
2010 Trabuco LG, Harrison CB, Schreiner E, Schulten K. Recognition of the regulatory nascent chain TnaC by the ribosome. Structure (London, England : 1993). 18: 627-37. PMID 20462496 DOI: 10.1016/j.str.2010.02.011  1
2010 Rajan A, Freddolino PL, Schulten K. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding. Plos One. 5: e9890. PMID 20419160 DOI: 10.1371/journal.pone.0009890  1
2010 Miao L, Schulten K. Probing a structural model of the nuclear pore complex channel through molecular dynamics. Biophysical Journal. 98: 1658-67. PMID 20409487 DOI: 10.1016/j.bpj.2009.12.4305  1
2010 Lee EH, Hsin J, von Castelmur E, Mayans O, Schulten K. Tertiary and secondary structure elasticity of a six-Ig titin chain. Biophysical Journal. 98: 1085-95. PMID 20303866 DOI: 10.1016/j.bpj.2009.12.4192  1
2010 Hsin J, Chandler DE, Gumbart J, Harrison CB, Sener M, Strumpfer J, Schulten K. Self-assembly of photosynthetic membranes. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 1154-9. PMID 20183845 DOI: 10.1002/cphc.200900911  1
2010 Stone JE, Kohlmeyer A, Vandivort KL, Schulten K. Immersive molecular visualization and interactive modeling with commodity hardware Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6454: 382-393. DOI: 10.1007/978-3-642-17274-8_38  1
2009 Aksimentiev A, Brunner RK, Cruz-Chú E, Comer J, Schulten K. Modeling Transport Through Synthetic Nanopores. Ieee Nanotechnology Magazine. 3: 20-28. PMID 21909347 DOI: 10.1109/MNANO.2008.931112  1
2009 Cruz-Chu ER, Ritz T, Siwy ZS, Schulten K. Molecular control of ionic conduction in polymer nanopores. Faraday Discussions. 143: 47-62; discussion 81. PMID 20334094 DOI: 10.1039/b906279n  1
2009 Sener M, Hsin J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides. Chemical Physics. 357: 188-197. PMID 20161332 DOI: 10.1016/j.chemphys.2009.01.003  1
2009 Hardy DJ, Stone JE, Schulten K. Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units. Parallel Computing. 35: 164-177. PMID 20161132 DOI: 10.1016/j.parco.2008.12.005  1
2009 Cruz-Chu ER, Aksimentiev A, Schulten K. Ionic Current Rectification Through Silica Nanopores. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 113: 1850. PMID 20126282 DOI: 10.1021/jp804724p  1
2009 Le L, Lee E, Schulten K, Truong TN. Molecular modeling of swine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 neuraminidases bound to Tamiflu and Relenza. Plos Currents. 1: RRN1015. PMID 20029609 DOI: 10.1371/currents.RRN1015  1
2009 Strümpfer J, Schulten K. Light harvesting complex II B850 excitation dynamics Journal of Chemical Physics. 131. PMID 20001083 DOI: 10.1063/1.3271348  1
2009 Chandler DE, Gumbart J, Stack JD, Chipot C, Schulten K. Membrane curvature induced by aggregates of LH2s and monomeric LH1s. Biophysical Journal. 97: 2978-84. PMID 19948127 DOI: 10.1016/j.bpj.2009.09.007  1
2009 Seidelt B, Innis CA, Wilson DN, Gartmann M, Armache JP, Villa E, Trabuco LG, Becker T, Mielke T, Schulten K, Steitz TA, Beckmann R. Structural insight into nascent polypeptide chain-mediated translational stalling. Science (New York, N.Y.). 326: 1412-5. PMID 19933110 DOI: 10.1126/science.1177662  1
2009 Becker T, Bhushan S, Jarasch A, Armache JP, Funes S, Jossinet F, Gumbart J, Mielke T, Berninghausen O, Schulten K, Westhof E, Gilmore R, Mandon EC, Beckmann R. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science (New York, N.Y.). 326: 1369-73. PMID 19933108 DOI: 10.1126/science.1178535  1
2009 Arkhipov A, Yin Y, Schulten K. Membrane-bending mechanism of amphiphysin N-BAR domains. Biophysical Journal. 97: 2727-35. PMID 19917226 DOI: 10.1016/j.bpj.2009.08.051  1
2009 Knapp JE, Pahl R, Cohen J, Nichols JC, Schulten K, Gibson QH, Srajer V, Royer WE. Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis. Structure (London, England : 1993). 17: 1494-504. PMID 19913484 DOI: 10.1016/j.str.2009.09.004  1
2009 Gumbart J, Trabuco LG, Schreiner E, Villa E, Schulten K. Regulation of the protein-conducting channel by a bound ribosome. Structure (London, England : 1993). 17: 1453-64. PMID 19913480 DOI: 10.1016/j.str.2009.09.010  1
2009 Hsin J, Chipot C, Schulten K. A glycophorin A-like framework for the dimerization of photosynthetic core complexes Journal of the American Chemical Society. 131: 17096-17098. PMID 19891482 DOI: 10.1021/ja905903n  1
2009 Freddolino PL, Schulten K. Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophysical Journal. 97: 2338-47. PMID 19843466 DOI: 10.1016/j.bpj.2009.08.012  1
2009 Lee EH, Hsin J, Sotomayor M, Comellas G, Schulten K. Discovery through the computational microscope. Structure (London, England : 1993). 17: 1295-306. PMID 19836330 DOI: 10.1016/j.str.2009.09.001  1
2009 Arkhipov A, Roos WH, Wuite GJL, Schulten K. Elucidating the mechanism behind irreversible deformation of viral capsids Biophysical Journal. 97: 2061-2069. PMID 19804738 DOI: 10.1016/j.bpj.2009.07.039  1
2009 Hsin J, Gumbart J, Trabuco LG, Villa E, Qian P, Hunter CN, Schulten K. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Biophysical Journal. 97: 321-9. PMID 19580770 DOI: 10.1016/j.bpj.2009.04.031  1
2009 Shih AY, Sligar SG, Schulten K. Maturation of high-density lipoproteins. Journal of the Royal Society, Interface / the Royal Society. 6: 863-71. PMID 19570799 DOI: 10.1098/rsif.2009.0173  1
2009 Solov'yov IA, Schulten K. Magnetoreception through cryptochrome may involve superoxide Biophysical Journal. 96: 4804-4813. PMID 19527640 DOI: 10.1016/j.bpj.2009.03.048  1
2009 Yin Y, Arkhipov A, Schulten K. Simulations of membrane tubulation by lattices of amphiphysin N-BAR domains. Structure (London, England : 1993). 17: 882-92. PMID 19523905 DOI: 10.1016/j.str.2009.03.016  1
2009 Freddolino PL, Park S, Roux B, Schulten K. Force field bias in protein folding simulations. Biophysical Journal. 96: 3772-80. PMID 19413983 DOI: 10.1016/j.bpj.2009.02.033  1
2009 Trabuco LG, Villa E, Schreiner E, Harrison CB, Schulten K. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods (San Diego, Calif.). 49: 174-80. PMID 19398010 DOI: 10.1016/j.ymeth.2009.04.005  1
2009 Maruthamuthu V, Schulten K, Leckband D. Elasticity and rupture of a multi-domain neural cell adhesion molecule complex. Biophysical Journal. 96: 3005-14. PMID 19383447 DOI: 10.1016/j.bpj.2008.12.3936  1
2009 Khalili-Araghi F, Gumbart J, Wen PC, Sotomayor M, Tajkhorshid E, Schulten K. Molecular dynamics simulations of membrane channels and transporters. Current Opinion in Structural Biology. 19: 128-37. PMID 19345092 DOI: 10.1016/j.sbi.2009.02.011  1
2009 Miao L, Schulten K. Transport-related structures and processes of the nuclear pore complex studied through molecular dynamics. Structure (London, England : 1993). 17: 449-59. PMID 19278659 DOI: 10.1016/j.str.2008.12.021  1
2009 Arkhipov A, Schulten K. Limits for reduction of effective focal volume in multiple-beam light microscopy Optics Express. 17: 2861-2870. PMID 19219190 DOI: 10.1364/OE.17.002861  1
2009 Mirsaidov U, Timp W, Zou X, Dimitrov V, Schulten K, Feinberg AP, Timp G. Nanoelectromechanics of methylated DNA in a synthetic nanopore. Biophysical Journal. 96: L32-4. PMID 19217843 DOI: 10.1016/j.bpj.2008.12.3760  1
2009 Hayashi S, Tajkhorshid E, Schulten K. Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation Biophysical Journal. 96: 403-416. PMID 19167292 DOI: 10.1016/j.bpj.2008.09.049  1
2009 Villa E, Sengupta J, Trabuco LG, LeBarron J, Baxter WT, Shaikh TR, Grassucci RA, Nissen P, Ehrenberg M, Schulten K, Frank J. Ribosome-induced changes in elongation factor Tu conformation control GTP hydrolysis. Proceedings of the National Academy of Sciences of the United States of America. 106: 1063-8. PMID 19122150 DOI: 10.1073/pnas.0811370106  1
2009 Stone JE, Saam J, Hardy DJ, Vandivort KL, Hwu WMW, Schulten K. High performance computation and display of molecular orbitals on and multi-core cpus Proceedings of 2nd Workshop On General Purpose Processing On Graphics Processing Units, Gpgpu-2. 9. DOI: 10.1145/1513895.1513897  1
2009 Archambault F, Chipot C, Soteras I, Luque FJ, Schulten K, Dehez F. Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions Journal of Chemical Theory and Computation. 5: 3022-3031. DOI: 10.1021/ct9004189  1
2009 Chen W, Lou J, Hsin J, Schulten K, Zhu C. In silico force-induced unbending of αvβ3 integrin Proceedings of the Asme Summer Bioengineering Conference 2009, Sbc2009. 1029-1030.  1
2008 Solov'yov IA, Chandler DE, Schulten K. Exploring the possibilities for radical pair effects in cryptochrome. Plant Signaling & Behavior. 3: 676-7. PMID 19704823  1
2008 Hsin J, Arkhipov A, Yin Y, Stone JE, Schulten K. Using VMD: An introductory tutorial Current Protocols in Bioinformatics. 5.7.1-5.7.48. PMID 19085979 DOI: 10.1002/0471250953.bi0507s24  1
2008 Aksimentiev A, Brunner R, Cohen J, Comer J, Cruz-Chu E, Hardy D, Rajan A, Shih A, Sigalov G, Yin Y, Schulten K. Computer modeling in biotechnology: a partner in development. Methods in Molecular Biology (Clifton, N.J.). 474: 181-234. PMID 19031067 DOI: 10.1007/978-1-59745-480-3_11  1
2008 Gumbart J, Schulten K. The roles of pore ring and plug in the secY protein-conducting channel Journal of General Physiology. 132: 709-719. PMID 19001142  1
2008 Vásquez V, Sotomayor M, Cordero-Morales J, Schulten K, Perozo E. A structural mechanism for MscS gating in lipid bilayers. Science (New York, N.Y.). 321: 1210-4. PMID 18755978 DOI: 10.1126/science.1159674  1
2008 Yao Y, Harrison CB, Freddolino PL, Schulten K, Mayer ML. Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. The Embo Journal. 27: 2158-70. PMID 18636091 DOI: 10.1038/emboj.2008.140  1
2008 Chandler DE, Hsin J, Harrison CB, Gumbart J, Schulten K. Intrinsic curvature properties of photosynthetic proteins in chromatophores. Biophysical Journal. 95: 2822-36. PMID 18515401 DOI: 10.1529/biophysj.108.132852  1
2008 Arkhipov A, Yin Y, Schulten K. Four-scale description of membrane sculpting by BAR domains Biophysical Journal. 95: 2806-2821. PMID 18515394 DOI: 10.1529/biophysj.108.132563  1
2008 Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure (London, England : 1993). 16: 673-83. PMID 18462672 DOI: 10.1016/j.str.2008.03.005  1
2008 Cohen J, Olsen KW, Schulten K. Finding gas migration pathways in proteins using implicit ligand sampling. Methods in Enzymology. 437: 439-57. PMID 18433641 DOI: 10.1016/S0076-6879(07)37022-5  1
2008 Freddolino PL, Liu F, Gruebele M, Schulten K. Ten-microsecond molecular dynamics simulation of a fast-folding WW domain. Biophysical Journal. 94: L75-7. PMID 18339748 DOI: 10.1529/biophysj.108.131565  1
2008 Rodrigues CI, Hardy DJ, Stone JE, Schulten K, Hwu WMW. GPU acceleration of cutoff pair potentials for molecular modeling applications Conference On Computing Frontiers - Proceedings of the 2008 Conference On Computing Frontiers, Cf'08. 273-282. DOI: 10.1145/1366230.1366277  1
2008 Phillips JC, Stone JE, Schulten K. Adapting a message-driven parallel application to GPU-accelerated clusters 2008 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis, Sc 2008. DOI: 10.1109/SC.2008.5214716  1
2007 Cui S, Yu J, Kühner F, Schulten K, Gaub HE. Double-stranded DNA dissociates into single strands when dragged into a poor solvent. Journal of the American Chemical Society. 129: 14710-6. PMID 17983226 DOI: 10.1021/ja074776c  1
2007 Hohng S, Zhou R, Nahas MK, Yu J, Schulten K, Lilley DM, Ha T. Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. Science (New York, N.Y.). 318: 279-83. PMID 17932299 DOI: 10.1126/science.1146113  1
2007 Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry. 28: 2618-40. PMID 17894371 DOI: 10.1002/jcc.20829  1
2007 Yu J, Ha T, Schulten K. How directional translocation is regulated in a DNA helicase motor. Biophysical Journal. 93: 3783-97. PMID 17704159 DOI: 10.1529/biophysj.107.109546  1
2007 Isgro TA, Schulten K. Cse1p-binding dynamics reveal a binding pattern for FG-repeat nucleoporins on transport receptors. Structure (London, England : 1993). 15: 977-91. PMID 17698002 DOI: 10.1016/j.str.2007.06.011  1
2007 Shih AY, Arkhipov A, Freddolino PL, Sligar SG, Schulten K. Assembly of lipids and proteins into lipoprotein particles. The Journal of Physical Chemistry. B. 111: 11095-104. PMID 17696388 DOI: 10.1021/jp072320b  1
2007 Cohen J, Schulten K. O2 migration pathways are not conserved across proteins of a similar fold. Biophysical Journal. 93: 3591-600. PMID 17693478 DOI: 10.1529/biophysj.107.108712  1
2007 Shih AY, Freddolino PL, Sligar SG, Schulten K. Disassembly of nanodiscs with cholate. Nano Letters. 7: 1692-6. PMID 17503871 DOI: 10.1021/nl0706906  1
2007 Johnson BJ, Cohen J, Welford RW, Pearson AR, Schulten K, Klinman JP, Wilmot CM. Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase Journal of Biological Chemistry. 282: 17767-17776. PMID 17409383 DOI: 10.1074/jbc.M701308200  1
2007 Wang Y, Cohen J, Boron WF, Schulten K, Tajkhorshid E. Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. Journal of Structural Biology. 157: 534-44. PMID 17306562 DOI: 10.1016/j.jsb.2006.11.008  1
2007 Solov'yov IA, Chandler DE, Schulten K. Magnetic field effects in Arabidopsis thaliana cryptochrome-1. Biophysical Journal. 92: 2711-26. PMID 17259272 DOI: 10.1529/biophysj.106.097139  1
2007 Isgro TA, Schulten K. Association of nuclear pore FG-repeat domains to NTF2 import and export complexes. Journal of Molecular Biology. 366: 330-45. PMID 17161424 DOI: 10.1016/j.jmb.2006.11.048  1
2007 Shih AY, Freddolino PL, Arkhipov A, Schulten K. Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Journal of Structural Biology. 157: 579-92. PMID 17070069 DOI: 10.1016/j.jsb.2006.08.006  1
2007 Chen H, Ilan B, Wu Y, Zhu F, Schulten K, Voth GA. Charge delocalization in proton channels, I: the aquaporin channels and proton blockage. Biophysical Journal. 92: 46-60. PMID 17056733 DOI: 10.1529/biophysj.106.091934  1
2006 Arkhipov A, Freddolino PL, Schulten K. Stability and dynamics of virus capsids described by coarse-grained modeling. Structure (London, England : 1993). 14: 1767-77. PMID 17161367 DOI: 10.1016/j.str.2006.10.003  1
2006 Puklin-Faucher E, Gao M, Schulten K, Vogel V. How the headpiece hinge angle is opened: New insights into the dynamics of integrin activation. The Journal of Cell Biology. 175: 349-60. PMID 17060501 DOI: 10.1083/jcb.200602071  1
2006 Arkhipov A, Freddolino PL, Imada K, Namba K, Schulten K. Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Biophysical Journal. 91: 4589-97. PMID 16997871 DOI: 10.1529/biophysj.106.093443  1
2006 Yu J, Yool AJ, Schulten K, Tajkhorshid E. Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1. Structure (London, England : 1993). 14: 1411-23. PMID 16962972 DOI: 10.1016/j.str.2006.07.006  1
2006 Dittrich M, Schulten K. PcrA helicase, a prototype ATP-driven molecular motor. Structure (London, England : 1993). 14: 1345-53. PMID 16962966 DOI: 10.1016/j.str.2006.06.017  1
2006 Freddolino PL, Dittrich M, Schulten K. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophysical Journal. 91: 3630-9. PMID 16935961 DOI: 10.1529/biophysj.106.088609  1
2006 Gao M, Sotomayor M, Villa E, Lee EH, Schulten K. Molecular mechanisms of cellular mechanics. Physical Chemistry Chemical Physics : Pccp. 8: 3692-706. PMID 16896432 DOI: 10.1039/b606019f  1
2006 Khalili-Araghi F, Tajkhorshid E, Schulten K. Dynamics of K+ ion conduction through Kv1.2. Biophysical Journal. 91: L72-4. PMID 16844753 DOI: 10.1529/biophysj.106.091926  1
2006 Yu J, Ha T, Schulten K. Structure-based model of the stepping motor of PcrA helicase. Biophysical Journal. 91: 2097-114. PMID 16815905 DOI: 10.1529/biophysj.106.088203  1
2006 Cohen J, Arkhipov A, Braun R, Schulten K. Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin. Biophysical Journal. 91: 1844-57. PMID 16751246 DOI: 10.1529/biophysj.106.085746  1
2006 Lu D, Aksimentiev A, Shih AY, Cruz-Chu E, Freddolino PL, Arkhipov A, Schulten K. The role of molecular modeling in bionanotechnology. Physical Biology. 3: S40-53. PMID 16582464 DOI: 10.1088/1478-3975/3/1/S05  1
2006 Lee EH, Gao M, Pinotsis N, Wilmanns M, Schulten K. Mechanical strength of the titin Z1Z2-telethonin complex. Structure (London, England : 1993). 14: 497-509. PMID 16531234 DOI: 10.1016/j.str.2005.12.005  1
2006 Freddolino PL, Arkhipov AS, Larson SB, McPherson A, Schulten K. Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure (London, England : 1993). 14: 437-49. PMID 16531228 DOI: 10.1016/j.str.2005.11.014  1
2006 Shih AY, Arkhipov A, Freddolino PL, Schulten K. Coarse grained protein-lipid model with application to lipoprotein particles. The Journal of Physical Chemistry. B. 110: 3674-84. PMID 16494423 DOI: 10.1021/jp0550816  1
2006 Gao M, Schulten K. Onset of anthrax toxin pore formation. Biophysical Journal. 90: 3267-79. PMID 16473908 DOI: 10.1529/biophysj.105.079376  1
2005 Li Y, Lu D, Schulten K, Ravaioli U, Rotkin SV. Screening of Water Dipoles Inside Finite-Length Armchair Carbon Nanotubes. Journal of Computational Electronics. 4: 161-165. PMID 18958297 DOI: 10.1007/s10825-005-7130-9  1
2005 Dittrich M, Freddolino PL, Schulten K. When light falls in LOV: a quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. The Journal of Physical Chemistry. B. 109: 13006-13. PMID 16852614 DOI: 10.1021/jp050943o  1
2005 Lu D, Li Y, Ravaioli U, Schulten K. Empirical nanotube model for biological applications. The Journal of Physical Chemistry. B. 109: 11461-7. PMID 16852403 DOI: 10.1021/jp050420g  1
2005 Dittrich M, Schulten K. Zooming in on ATP hydrolysis in F1. Journal of Bioenergetics and Biomembranes. 37: 441-4. PMID 16691480 DOI: 10.1007/s10863-005-9487-7  1
2005 Lu D, Li Y, Ravaioli U, Schulten K. Ion-nanotube terahertz oscillator. Physical Review Letters. 95: 246801. PMID 16384404 DOI: 10.1103/PhysRevLett.95.246801  1
2005 Isgro TA, Schulten K. Binding dynamics of isolated nucleoporin repeat regions to importin-beta. Structure (London, England : 1993). 13: 1869-79. PMID 16338415 DOI: 10.1016/j.str.2005.09.007  1
2005 Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. 26: 1781-802. PMID 16222654 DOI: 10.1002/jcc.20289  1
2005 Cohen J, Kim K, King P, Seibert M, Schulten K. Finding gas diffusion pathways in proteins: application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects. Structure (London, England : 1993). 13: 1321-9. PMID 16154089 DOI: 10.1016/j.str.2005.05.013  1
2005 Villa E, Balaeff A, Schulten K. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proceedings of the National Academy of Sciences of the United States of America. 102: 6783-8. PMID 15863616 DOI: 10.1073/pnas.0409387102  1
2005 Cohen J, Kim K, Posewitz M, Ghirardi ML, Schulten K, Seibert M, King P. Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase. Biochemical Society Transactions. 33: 80-2. PMID 15667271 DOI: 10.1042/BST0330080  1
2005 Ghirardi ML, King PW, Posewitz MC, Maness PC, Fedorov A, Kim K, Cohen J, Schulten K, Seibert M. Approaches to developing biological H(2)-photoproducing organisms and processes. Biochemical Society Transactions. 33: 70-2. PMID 15667268 DOI: 10.1042/BST0330070  1
2004 Yu J, Ha T, Schulten K. Conformational model of the Holliday junction transition deduced from molecular dynamics simulations. Nucleic Acids Research. 32: 6683-95. PMID 15613597 DOI: 10.1093/nar/gkh1006  1
2004 Zhu F, Tajkhorshid E, Schulten K. Collective diffusion model for water permeation through microscopic channels. Physical Review Letters. 93: 224501. PMID 15601094 DOI: 10.1103/PhysRevLett.93.224501  1
2004 Gao M, Schulten K. Integrin activation in vivo and in silico. Structure (London, England : 1993). 12: 2096-8. PMID 15576022 DOI: 10.1016/j.str.2004.11.005  1
2004 Craig D, Gao M, Schulten K, Vogel V. Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force. Structure (London, England : 1993). 12: 2049-58. PMID 15530369 DOI: 10.1016/j.str.2004.09.009  1
2004 Dittrich M, Hayashi S, Schulten K. ATP hydrolysis in the betaTP and betaDP catalytic sites of F1-ATPase. Biophysical Journal. 87: 2954-67. PMID 15315950 DOI: 10.1529/biophysj.104.046128  1
2004 Braun R, Engelman DM, Schulten K. Molecular Dynamics Simulations of Micelle Formation around Dimeric Glycophorin A Transmembrane Helices. Biophysical Journal. 87: 754-63. PMID 15298884 DOI: 10.1529/biophysj.104.040279  1
2004 Sener MK, Park S, Lu D, Damjanovic A, Ritz T, Fromme P, Schulten K. Excitation migration in trimeric cyanobacterial photosystem I. The Journal of Chemical Physics. 120: 11183-95. PMID 15268148 DOI: 10.1063/1.1739400  1
2004 Park S, Schulten K. Calculating potentials of mean force from steered molecular dynamics simulations. The Journal of Chemical Physics. 120: 5946-61. PMID 15267476 DOI: 10.1063/1.1651473  1
2004 Cohen J, Schulten K. Mechanism of anionic conduction across ClC. Biophysical Journal. 86: 836-45. PMID 14747319 DOI: 10.1016/S0006-3495(04)74159-4  1
2004 Craig D, Gao M, Schulten K, Vogel V. Tuning the mechanical stability of fibronectin type III modules through sequence variations. Structure (London, England : 1993). 12: 21-30. PMID 14725762 DOI: 10.1016/j.str.2003.11.024  1
2004 Zhu F, Tajkhorshid E, Schulten K. Theory and simulation of water permeation in aquaporin-1. Biophysical Journal. 86: 50-7. PMID 14695248 DOI: 10.1016/S0006-3495(04)74082-5  1
2003 Gao M, Craig D, Lequin O, Campbell ID, Vogel V, Schulten K. Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates. Proceedings of the National Academy of Sciences of the United States of America. 100: 14784-9. PMID 14657397 DOI: 10.1073/pnas.2334390100  1
2003 Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, Zhu F, Schulten K. Large scale simulation of protein mechanics and function. Advances in Protein Chemistry. 66: 195-247. PMID 14631820 DOI: 10.1016/S0065-3233(03)66006-7  1
2003 Lu D, Grayson P, Schulten K. Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF. Biophysical Journal. 85: 2977-87. PMID 14581200 DOI: 10.1016/S0006-3495(03)74718-3  1
2003 Dittrich M, Hayashi S, Schulten K. On the mechanism of ATP hydrolysis in F1-ATPase. Biophysical Journal. 85: 2253-66. PMID 14507690 DOI: 10.1016/S0006-3495(03)74650-5  1
2003 Zhu F, Schulten K. Water and proton conduction through carbon nanotubes as models for biological channels. Biophysical Journal. 85: 236-44. PMID 12829479 DOI: 10.1016/S0006-3495(03)74469-5  1
2002 Gao M, Lu H, Schulten K. Unfolding of titin domains studied by molecular dynamics simulations. Journal of Muscle Research and Cell Motility. 23: 513-21. PMID 12785101 DOI: 10.1023/A:1023466608163  1
2002 Ritz T, Damjanović A, Schulten K. The quantum physics of photosynthesis. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 3: 243-8. PMID 12503169 DOI: 10.1002/1439-7641(20020315)3:3<243::AID-CPHC243>3.0.CO;2-Y  1
2002 Gao M, Wilmanns M, Schulten K. Steered molecular dynamics studies of titin I1 domain unfolding. Biophysical Journal. 83: 3435-45. PMID 12496110 DOI: 10.1016/S0006-3495(02)75343-5  1
2002 Gao M, Craig D, Vogel V, Schulten K. Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics. Journal of Molecular Biology. 323: 939-50. PMID 12417205 DOI: 10.1016/S0022-2836(02)01001-X  1
2002 Braun R, Sarikaya M, Schulten K. Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics. Journal of Biomaterials Science. Polymer Edition. 13: 747-57. PMID 12296441 DOI: 10.1163/156856202760197384  1
2002 Zhu F, Tajkhorshid E, Schulten K. Pressure-induced water transport in membrane channels studied by molecular dynamics. Biophysical Journal. 83: 154-60. PMID 12080108 DOI: 10.1016/S0006-3495(02)75157-6  1
2002 Hu X, Ritz T, Damjanović A, Autenrieth F, Schulten K. Photosynthetic apparatus of purple bacteria. Quarterly Reviews of Biophysics. 35: 1-62. PMID 11997980 DOI: 10.1017/S0033583501003754  1
2002 Jensen MØ, Park S, Tajkhorshid E, Schulten K. Energetics of glycerol conduction through aquaglyceroporin GlpF. Proceedings of the National Academy of Sciences of the United States of America. 99: 6731-6. PMID 11997475 DOI: 10.1073/pnas.102649299  1
2002 Damjanović A, Kosztin I, Kleinekathöfer U, Schulten K. Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 031919. PMID 11909121 DOI: 10.1103/PhysRevE.65.031919  0.84
2001 Gao M, Lu H, Schulten K. Simulated refolding of stretched titin immunoglobulin domains. Biophysical Journal. 81: 2268-77. PMID 11566797 DOI: 10.1016/S0006-3495(01)75874-2  1
2001 Zhu F, Tajkhorshid E, Schulten K. Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer. Febs Letters. 504: 212-8. PMID 11532456  1
2001 Isralewitz B, Baudry J, Gullingsrud J, Kosztin D, Schulten K. Steered molecular dynamics investigations of protein function. Journal of Molecular Graphics & Modelling. 19: 13-25. PMID 11381523 DOI: 10.1016/S1093-3263(00)00133-9  1
2001 Isralewitz B, Gao M, Schulten K. Steered molecular dynamics and mechanical functions of proteins. Current Opinion in Structural Biology. 11: 224-30. PMID 11297932 DOI: 10.1016/S0959-440X(00)00194-9  1
2000 Ritz T, Damjanović A, Schulten K, Zhang JP, Koyama Y. Efficient light harvesting through carotenoids. Photosynthesis Research. 66: 125-44. PMID 16228415 DOI: 10.1023/A:1010750332320  1
2000 Damjanović A, Ritz T, Schulten K. Excitation transfer in the peridinin-chlorophyll-protein of Amphidinium carterae. Biophysical Journal. 79: 1695-705. PMID 11023878 DOI: 10.1016/S0006-3495(00)76422-8  1
2000 Lu H, Krammer A, Isralewitz B, Vogel V, Schulten K. Computer modeling of force-induced titin domain unfolding. Advances in Experimental Medicine and Biology. 481: 143-60; discussion 1. PMID 10987071  1
1999 Krammer A, Lu H, Isralewitz B, Schulten K, Vogel V. Forced unfolding of the fibronectin type III module reveals a tensile molecular recognition switch. Proceedings of the National Academy of Sciences of the United States of America. 96: 1351-6. PMID 9990027 DOI: 10.1073/pnas.96.4.1351  1
1998 Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K. Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation. Biophysical Journal. 75: 662-71. PMID 9675168 DOI: 10.1016/S0006-3495(98)77556-3  1
1998 Hu X, Damjanović A, Ritz T, Schulten K. Architecture and mechanism of the light-harvesting apparatus of purple bacteria. Proceedings of the National Academy of Sciences of the United States of America. 95: 5935-41. PMID 9600895 DOI: 10.1073/pnas.95.11.5935  1
1997 Isralewitz B, Izrailev S, Schulten K. Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophysical Journal. 73: 2972-9. PMID 9414212 DOI: 10.1016/S0006-3495(97)78326-7  1
1993 Martinetz TM, Berkovich SG, Schulten KJ. ;Neural-gas' network for vector quantization and its application to time-series prediction. Ieee Transactions On Neural Networks / a Publication of the Ieee Neural Networks Council. 4: 558-69. PMID 18267757 DOI: 10.1109/72.238311  1
1992 Treutlein H, Schulten K, Brünger AT, Karplus M, Deisenhofer J, Michel H. Chromophore-protein interactions and the function of the photosynthetic reaction center: a molecular dynamics study. Proceedings of the National Academy of Sciences of the United States of America. 89: 75-9. PMID 1729721  1
1990 Martinetz TM, Ritter HJ, Schulten KJ. Three-dimensional neural net for learning visuomotor coordination of a robot arm. Ieee Transactions On Neural Networks / a Publication of the Ieee Neural Networks Council. 1: 131-6. PMID 18282830 DOI: 10.1109/72.80212  1
1987 Nadler W, Brünger AT, Schulten K, Karplus M. Molecular and stochastic dynamics of proteins. Proceedings of the National Academy of Sciences of the United States of America. 84: 7933-7. PMID 3479772  0.44
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