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Vijay S. Pande - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
theoretical methods to understand the physical properties of biological molecules
Website:
https://profiles.stanford.edu/vijay-pande
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347 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry. B. PMID 38154096 DOI: 10.1021/acs.jpcb.3c06662  0.657
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. Arxiv. PMID 37986730  0.587
2023 Voelz VA, Pande VS, Bowman GR. Folding@home: achievements from over twenty years of citizen science herald the exascale era. Arxiv. PMID 36994157  0.758
2023 Voelz VA, Pande VS, Bowman GR. Folding@home: Achievements from over 20 years of citizen science herald the exascale era. Biophysical Journal. PMID 36945779 DOI: 10.1016/j.bpj.2023.03.028  0.757
2020 McKiernan KA, Koster AK, Maduke M, Pande VS. Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating. Plos Computational Biology. 16: e1007530. PMID 32226009 DOI: 10.1371/Journal.Pcbi.1007530  0.358
2020 Dalton K, Lopez T, Pande V, Frydman J. REP-X: An Evolution-guided Strategy for the Rational Design of Cysteine-less Protein Variants. Scientific Reports. 10: 2193. PMID 32042106 DOI: 10.1038/S41598-020-58794-X  0.326
2020 Kostrz DN, Wayment-Steele HK, Wang J, Follenfant M, Pande VS, Triller A, Specht CG, Strick TR, Gosse C. A Modular DNA Scaffold to Study Protein-Protein Interactions at Single-Molecule Resolution Biophysical Journal. 118: 187a. DOI: 10.1016/J.Bpj.2019.11.1138  0.3
2019 Kostrz D, Wayment-Steele HK, Wang JL, Follenfant M, Pande VS, Strick TR, Gosse C. A modular DNA scaffold to study protein-protein interactions at single-molecule resolution. Nature Nanotechnology. PMID 31548690 DOI: 10.1038/S41565-019-0542-7  0.323
2018 Feinberg EN, Sur D, Wu Z, Husic BE, Mai H, Li Y, Sun S, Yang J, Ramsundar B, Pande VS. PotentialNet for Molecular Property Prediction. Acs Central Science. 4: 1520-1530. PMID 30555904 DOI: 10.1021/Acscentsci.8B00507  0.742
2018 Wayment-Steele HK, Pande VS. Note: Variational encoding of protein dynamics benefits from maximizing latent autocorrelation. The Journal of Chemical Physics. 149: 216101. PMID 30525733 DOI: 10.1063/1.5043303  0.391
2018 Krylov A, Windus TL, Barnes T, Marin-Rimoldi E, Nash JA, Pritchard B, Smith DGA, Altarawy D, Saxe P, Clementi C, Crawford TD, Harrison RJ, Jha S, Pande VS, Head-Gordon T. Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. The Journal of Chemical Physics. 149: 180901. PMID 30441927 DOI: 10.1063/1.5052551  0.321
2018 Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL. Bayesian analysis of isothermal titration calorimetry for binding thermodynamics. Plos One. 13: e0203224. PMID 30212471 DOI: 10.1371/Journal.Pone.0203224  0.583
2018 Sultan MM, Pande VS. Automated design of collective variables using supervised machine learning. The Journal of Chemical Physics. 149: 094106. PMID 30195289 DOI: 10.1063/1.5029972  0.371
2018 Sinitskiy AV, Pande VS. Computer Simulations Predict High Structural Heterogeneity of Functional State of NMDA Receptors. Biophysical Journal. PMID 30029773 DOI: 10.1016/J.Bpj.2018.06.023  0.463
2018 Hernández CX, Wayment-Steele HK, Sultan MM, Husic BE, Pande VS. Variational encoding of complex dynamics. Physical Review. E. 97: 062412. PMID 30011547 DOI: 10.1103/Physreve.97.062412  0.804
2018 Sultan MM, Kiss G, Pande VS. Towards simple kinetic models of functional dynamics for a kinase subfamily. Nature Chemistry. PMID 29988151 DOI: 10.1038/S41557-018-0077-9  0.402
2018 Wagoner JA, Pande VS. Communication: Adaptive boundaries in multiscale simulations. The Journal of Chemical Physics. 148: 141104. PMID 29655340 DOI: 10.1063/1.5025826  0.393
2018 Sultan MM, Wayment-Steele HK, Pande VS. Transferable neural networks for enhanced sampling of protein dynamics. Journal of Chemical Theory and Computation. PMID 29529369 DOI: 10.1021/Acs.Jctc.8B00025  0.361
2018 Yang H, Staveness D, Ryckbosch SM, Axtman AD, Loy BA, Barnes AB, Pande VS, Schaefer J, Wender PA, Cegelski L. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. Acs Central Science. 4: 89-96. PMID 29392180 DOI: 10.1021/Acscentsci.7B00475  0.375
2018 Sinitskiy AV, Pande VS. Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics. The Journal of Chemical Physics. 148: 044111. PMID 29390806 DOI: 10.1063/1.5005058  0.426
2018 Husic BE, Pande VS. Markov State Models: From an Art to a Science. Journal of the American Chemical Society. PMID 29323881 DOI: 10.1021/Jacs.7B12191  0.784
2018 Barati Farimani A, Feinberg E, Pande V. Binding Pathway of Opiates to μ-Opioid Receptors Revealed by Machine Learning Biophysical Journal. 114: 62a-63a. DOI: 10.1016/J.Bpj.2017.11.390  0.301
2018 Feinberg EN, Pande VS, Barati Farimani A, Hernandez CX. Kinetic Machine Learning Unravels Ligand-Directed Conformational Change of μ Opioid Receptor Biophysical Journal. 114: 56a. DOI: 10.1016/J.Bpj.2017.11.359  0.576
2018 Wayment-Steele HK, Hernandez CX, Husic BE, Pande VS. Hierarchical Clustering of Markov State Models Reveals Sequence Effects in p53-CTD Dynamic Behavior Biophysical Journal. 114: 561a. DOI: 10.1016/J.Bpj.2017.11.3066  0.786
2018 Hernández CX, Wayment-Steele H, Pande VS. On the Origins of Regulated Disorder within the C-Terminus of P53 Biophysical Journal. 114: 428a. DOI: 10.1016/J.Bpj.2017.11.2376  0.544
2018 Sinitskiy AV, Subedi GP, Barb AW, Pande VS. Glycan-Protein Interactions in NMDA Receptors Revealed with Computational Modeling and NMR Spectroscopy Biophysical Journal. 114: 338a. DOI: 10.1016/J.Bpj.2017.11.1889  0.302
2018 Sultan MM, Pande V. Lessons from 8 Milliseconds of Aggregated Kinase Molecular Dynamics Simulations Biophysical Journal. 114: 233a. DOI: 10.1016/J.Bpj.2017.11.1298  0.364
2018 Husic BE, McKiernan KA, Pande VS. Understanding how Beta-Hairpins Fold using Molecular Dynamics Simulations in Multiple Force Fields Biophysical Journal. 114: 208a-209a. DOI: 10.1016/J.Bpj.2017.11.1167  0.765
2017 Husic BE, McKiernan KA, Wayment-Steele HK, Sultan MM, Pande VS. A minimum variance clustering approach produces robust and interpretable coarse-grained models. Journal of Chemical Theory and Computation. PMID 29253336 DOI: 10.1021/Acs.Jctc.7B01004  0.791
2017 Sultan MM, Denny RA, Unwalla R, Lovering F, Pande VS. Millisecond dynamics of BTK reveal kinome-wide conformational plasticity within the apo kinase domain. Scientific Reports. 7: 15604. PMID 29142210 DOI: 10.1038/S41598-017-10697-0  0.411
2017 Husic BE, Pande VS. Note: MSM lag time cannot be used for variational model selection. The Journal of Chemical Physics. 147: 176101. PMID 29117698 DOI: 10.1063/1.5002086  0.741
2017 Lee FL, Barati Farimani A, Gu KL, Yan H, Toney MF, Bao Z, Pande VS. Solution-Phase Conformation and Dynamics of Conjugated Isoindigo-Based Donor-Acceptor Polymer Single Chains. The Journal of Physical Chemistry Letters. PMID 29065685 DOI: 10.1021/Acs.Jpclett.7B02360  0.356
2017 Sinitskiy AV, Pande VS. Simulated Dynamics of Glycans on Ligand-Binding Domain of NMDA Receptors Reveals Strong Dynamic Coupling between Glycans and Protein Core. Journal of Chemical Theory and Computation. PMID 29019687 DOI: 10.1021/Acs.Jctc.7B00817  0.355
2017 Sultan MM, Pande VS. Transfer Learning from Markov Models Leads to Efficient Sampling of Related Systems. The Journal of Physical Chemistry. B. PMID 28938073 DOI: 10.1021/Acs.Jpcb.7B06896  0.371
2017 McKiernan KA, Husic BE, Pande VS. Modeling the mechanism of CLN025 beta-hairpin formation. The Journal of Chemical Physics. 147: 104107. PMID 28915754 DOI: 10.1063/1.4993207  0.77
2017 Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659. PMID 28746339 DOI: 10.1371/Journal.Pcbi.1005659  0.752
2017 M Sultan M, Pande VS. tICA-Metadynamics: Accelerating Metadynamics by using kinetically selected collective variables. Journal of Chemical Theory and Computation. PMID 28383914 DOI: 10.1021/Acs.Jctc.7B00182  0.39
2017 Sinitskiy AV, Stanley NH, Hackos DH, Hanson JE, Sellers BD, Pande VS. Computationally Discovered Potentiating Role of Glycans on NMDA Receptors. Scientific Reports. 7: 44578. PMID 28378791 DOI: 10.1038/Srep44578  0.336
2017 Harrigan MP, McKiernan KA, Shanmugasundaram V, Denny RA, Pande VS. Markov modeling reveals novel intracellular modulation of the human TREK-2 selectivity filter. Scientific Reports. 7: 632. PMID 28377596 DOI: 10.1038/S41598-017-00256-Y  0.355
2017 Wang LP, McKiernan KA, Gomes J, Beauchamp KA, Head-Gordon T, Rice JE, Swope WC, Martínez TJ, Pande VS. Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15. The Journal of Physical Chemistry. B. PMID 28306259 DOI: 10.1021/Acs.Jpcb.7B02320  0.816
2017 Shi J, Nobrega RP, Schwantes C, Kathuria SV, Bilsel O, Matthews CR, Lane TJ, Pande VS. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. Scientific Reports. 7: 44116. PMID 28272524 DOI: 10.1038/Srep44116  0.449
2017 Ryckbosch SM, Wender PA, Pande VS. Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes. Nature Communications. 8: 6. PMID 28232750 DOI: 10.1038/S41467-016-0015-8  0.336
2017 Husic BE, Pande VS. Ward clustering improves cross-validated Markov state models of protein folding. Journal of Chemical Theory and Computation. PMID 28195713 DOI: 10.1021/Acs.Jctc.6B01238  0.743
2017 Zhang B, Kilburg D, Eastman P, Pande VS, Gallicchio E. Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units. Journal of Computational Chemistry. PMID 28160511 DOI: 10.1002/Jcc.24745  0.317
2017 McGibbon RT, Husic BE, Pande VS. Identification of simple reaction coordinates from complex dynamics. The Journal of Chemical Physics. 146: 044109. PMID 28147508 DOI: 10.1063/1.4974306  0.762
2017 Harrigan MP, Sultan MM, Hernández CX, Husic BE, Eastman P, Schwantes CR, Beauchamp KA, McGibbon RT, Pande VS. MSMBuilder: Statistical Models for Biomolecular Dynamics. Biophysical Journal. 112: 10-15. PMID 28076801 DOI: 10.1016/J.Bpj.2016.10.042  0.822
2016 Husic BE, McGibbon RT, Sultan MM, Pande VS. Optimized parameter selection reveals trends in Markov state models for protein folding. The Journal of Chemical Physics. 145: 194103. PMID 27875868 DOI: 10.1063/1.4967809  0.795
2016 McKiernan KA, Wang LP, Pande VS. Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field. Journal of Chemical Theory and Computation. PMID 27786477 DOI: 10.1021/Acs.Jctc.6B00801  0.637
2016 Subramanian G, Ramsundar B, Pande VS, Denny RA. Computational Modeling of β-secretase 1 (BACE-1) Inhibitors using Ligand Based Approaches. Journal of Chemical Information and Modeling. PMID 27689393 DOI: 10.1021/Acs.Jcim.6B00290  0.319
2016 Albaugh A, Boateng HA, Bradshaw RT, Demerdash ON, Dziedzic J, Mao Y, Margul DT, Swails JM, Zeng Q, Case DA, Eastman PK, Essex JW, Head-Gordon M, Pande VS, Ponder JW, et al. Advanced Potential Energy Surfaces for Molecular Simulation. The Journal of Physical Chemistry. B. PMID 27513316 DOI: 10.1021/Acs.Jpcb.6B06414  0.556
2016 Shukla D, Peck A, Pande VS. Corrigendum: Conformational heterogeneity of the calmodulin binding interface. Nature Communications. 7: 12318. PMID 27506931 DOI: 10.1038/Ncomms12318  0.636
2016 Meng Y, Shukla D, Pande VS, Roux B. Transition path theory analysis of c-Src kinase activation. Proceedings of the National Academy of Sciences of the United States of America. PMID 27482115 DOI: 10.1073/Pnas.1602790113  0.614
2016 Bhowmick A, Brookes DH, Yost S, Dyson HJ, Forman-Kay JD, Gunter D, Head-Gordon M, Hura GL, Pande VS, Wemmer DE, Wright PE, Head-Gordon T. Finding Our Way in the Dark Proteome. Journal of the American Chemical Society. PMID 27387657 DOI: 10.1021/Jacs.6B06543  0.571
2016 Peck A, Sunden F, Andrews LD, Pande VS, Herschlag D. Tungstate as a transition state analog for catalysis by alkaline phosphatase. Journal of Molecular Biology. PMID 27189921 DOI: 10.1016/J.Jmb.2016.05.007  0.327
2016 Schwantes CR, Shukla D, Pande VS. Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2. Biophysical Journal. 110: 1716-9. PMID 27119632 DOI: 10.1016/J.Bpj.2016.03.026  0.655
2016 Dodani SC, Kiss G, Cahn JK, Su Y, Pande VS, Arnold FH. Discovery of a regioselectivity switch in nitrating P450s guided by molecular dynamics simulations and Markov models. Nature Chemistry. 8: 419-25. PMID 27102675 DOI: 10.1038/Nchem.2474  0.391
2016 Shukla D, Peck A, Pande VS. Conformational heterogeneity of the calmodulin binding interface. Nature Communications. 7: 10910. PMID 27040077 DOI: 10.1038/Ncomms10910  0.621
2016 Feinberg E, Pande V. Statistical Learning and Docking Recover the Reaction Coordinates of a GPCR Biophysical Journal. 110: 61a. DOI: 10.1016/J.Bpj.2015.11.394  0.368
2016 Sultan MM, Pande V. Computational Evaluation of Mutational Effects on Kinase Dynamics Biophysical Journal. 110: 325a. DOI: 10.1016/J.Bpj.2015.11.1745  0.367
2015 Wang LP, McGibbon RT, Pande VS, Martínez TJ. Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways. Journal of Chemical Theory and Computation. PMID 26683346 DOI: 10.1021/Acs.Jctc.5B00830  0.73
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935  0.392
2015 Harrigan MP, Shukla D, Pande VS. Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics. Journal of Chemical Theory and Computation. 11: 1094-101. PMID 26579759 DOI: 10.1021/Ct5010017  0.661
2015 Weber JK, Pande VS. Potential-Based Dynamical Reweighting for Markov State Models of Protein Dynamics. Journal of Chemical Theory and Computation. 11: 2412-20. PMID 26575541 DOI: 10.1021/Acs.Jctc.5B00031  0.463
2015 Schwantes CR, Pande VS. Modeling Molecular Kinetics with tICA and the Kernel Trick. Journal of Chemical Theory and Computation. 11: 600-608. PMID 26528090 DOI: 10.1021/Ct5007357  0.468
2015 McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang LP, Lane TJ, Pande VS. MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories. Biophysical Journal. 109: 1528-32. PMID 26488642 DOI: 10.1016/J.Bpj.2015.08.015  0.766
2015 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry. 7: 759. PMID 26291949 DOI: 10.1038/Nchem.2272  0.784
2015 Weber JK, Shukla D, Pande VS. Heat dissipation guides activation in signaling proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 26240354 DOI: 10.1073/Pnas.1501804112  0.656
2015 McGibbon RT, Pande VS. Efficient maximum likelihood parameterization of continuous-time Markov processes. The Journal of Chemical Physics. 143: 034109. PMID 26203016 DOI: 10.1063/1.4926516  0.373
2015 Qi R, Wang LP, Wang Q, Pande VS, Ren P. United polarizable multipole water model for molecular mechanics simulation. The Journal of Chemical Physics. 143: 014504. PMID 26156485 DOI: 10.1063/1.4923338  0.663
2015 Eastman P, Pande VS. OpenMM: A Hardware Independent Framework for Molecular Simulations. Computing in Science & Engineering. 12: 34-39. PMID 26146490 DOI: 10.1109/Mcse.2010.27  0.37
2015 Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan MF, Pande VS, Kern D. Free energy landscape of activation in a signalling protein at atomic resolution. Nature Communications. 6: 7284. PMID 26073309 DOI: 10.1038/Ncomms8284  0.394
2015 Vanatta DK, Shukla D, Lawrenz M, Pande VS. A network of molecular switches controls the activation of the two-component response regulator NtrC. Nature Communications. 6: 7283. PMID 26073186 DOI: 10.1038/Ncomms8283  0.673
2015 Weber JK, Pande VS. Percolation-like phase transitions in network models of protein dynamics. The Journal of Chemical Physics. 142: 215105. PMID 26049529 DOI: 10.1063/1.4921989  0.355
2015 Shukla D, Lawrenz M, Pande VS. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches. Methods in Enzymology. 557: 551-72. PMID 25950981 DOI: 10.1016/Bs.Mie.2014.12.007  0.642
2015 Weber JK, Pande VS. Entropy-production-driven oscillators in simple nonequilibrium networks. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 032136. PMID 25871083 DOI: 10.1103/Physreve.91.032136  0.353
2015 McGibbon RT, Pande VS. Variational cross-validation of slow dynamical modes in molecular kinetics. The Journal of Chemical Physics. 142: 124105. PMID 25833563 DOI: 10.1063/1.4916292  0.374
2015 Dalton KM, Frydman J, Pande VS. The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation. Plos One. 10: e0117724. PMID 25822285 DOI: 10.1371/Journal.Pone.0117724  0.436
2015 Laury ML, Wang LP, Pande VS, Head-Gordon T, Ponder JW. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model. The Journal of Physical Chemistry. B. 119: 9423-37. PMID 25683601 DOI: 10.1021/Jp510896N  0.638
2015 Shukla D, Hernández CX, Weber JK, Pande VS. Markov state models provide insights into dynamic modulation of protein function. Accounts of Chemical Research. 48: 414-22. PMID 25625937 DOI: 10.1021/Ar5002999  0.779
2015 Lawrenz M, Shukla D, Pande VS. Cloud computing approaches for prediction of ligand binding poses and pathways. Scientific Reports. 5: 7918. PMID 25608737 DOI: 10.1038/Srep07918  0.637
2015 Vanatta DK, Shukla D, Lawrenz M, Pande VS. A network of molecular switches controls the activation of the two-component response regulator NtrC Nature Communications. 6. DOI: 10.1038/ncomms8283  0.481
2015 Harrigan MP, Shukla D, Pande VS. Conserve water: A method for the analysis of solvent in molecular dynamics Journal of Chemical Theory and Computation. 11: 1094-1101. DOI: 10.1021/ct5010017  0.553
2015 Pontiggia F, Pachov DV, Clarkson MW, Villali J, Hagan MF, Pande VS, Kern D. Activation Mechanism of a Signaling Protein at Atomic Resolution Biophysical Journal. 108: 376a. DOI: 10.1016/J.Bpj.2014.11.2064  0.42
2015 Wagoner JA, Dill K, Pande V. Adaptive Boundaries in Multi-Resolution Simulations Biophysical Journal. 108: 182a. DOI: 10.1016/J.Bpj.2014.11.1007  0.585
2015 Shukla D, Lawrenz M, Pande VS. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches Methods in Enzymology. DOI: 10.1016/bs.mie.2014.12.007  0.537
2014 Wang LP, Martinez TJ, Pande VS. Building Force Fields: An Automatic, Systematic, and Reproducible Approach. The Journal of Physical Chemistry Letters. 5: 1885-91. PMID 26273869 DOI: 10.1021/Jz500737M  0.713
2014 Sultan MM, Kiss G, Shukla D, Pande VS. Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 10: 5217-5223. PMID 25516725 DOI: 10.1021/Ct500353M  0.674
2014 Wang LP, Titov A, McGibbon R, Liu F, Pande VS, Martínez TJ. Discovering chemistry with an ab initio nanoreactor. Nature Chemistry. 6: 1044-8. PMID 25411881 DOI: 10.1038/Nchem.2099  0.716
2014 Schwantes CR, McGibbon RT, Pande VS. Perspective: Markov models for long-timescale biomolecular dynamics. The Journal of Chemical Physics. 141: 090901. PMID 25194354 DOI: 10.1063/1.4895044  0.445
2014 Weber JK, Jack RL, Schwantes CR, Pande VS. Dynamical phase transitions reveal amyloid-like states on protein folding landscapes. Biophysical Journal. 107: 974-82. PMID 25140433 DOI: 10.1016/J.Bpj.2014.06.046  0.431
2014 Lapidus LJ, Acharya S, Schwantes CR, Wu L, Shukla D, King M, DeCamp SJ, Pande VS. Complex pathways in folding of protein G explored by simulation and experiment. Biophysical Journal. 107: 947-55. PMID 25140430 DOI: 10.1016/J.Bpj.2014.06.037  0.683
2014 McGibbon RT, Schwantes CR, Pande VS. Statistical model selection for Markov models of biomolecular dynamics Journal of Physical Chemistry B. 118: 6475-6481. PMID 24738580 DOI: 10.1021/Jp411822R  0.442
2014 Beauchamp KA, Pande VS, Das R. Bayesian energy landscape tilting: Towards concordant models of molecular ensembles Biophysical Journal. 106: 1381-1390. PMID 24655513 DOI: 10.1016/J.Bpj.2014.02.009  0.453
2014 Baiz CR, Lin YS, Peng CS, Beauchamp KA, Voelz VA, Pande VS, Tokmakoff A. A molecular interpretation of 2D IR protein folding experiments with Markov state models. Biophysical Journal. 106: 1359-70. PMID 24655511 DOI: 10.1016/J.Bpj.2014.02.008  0.716
2014 Shukla D, Meng Y, Roux B, Pande VS. Activation pathway of Src kinase reveals intermediate states as targets for drug design. Nature Communications. 5: 3397. PMID 24584478 DOI: 10.1038/Ncomms4397  0.628
2014 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways Nature Chemistry. 6: 15-21. PMID 24345941 DOI: 10.1038/Nchem.1821  0.82
2014 Pande VS. Understanding protein folding using markov state models Advances in Experimental Medicine and Biology. 797: 101-106. PMID 24297278 DOI: 10.1007/978-94-007-7606-7_8  0.454
2014 Bowman GR, Pande VS, Noé F. Introduction and overview of this book Advances in Experimental Medicine and Biology. 797: 1-6. PMID 24297271 DOI: 10.1007/978-94-007-7606-7_1  0.653
2014 Kearnes SM, Haque IS, Pande VS. SCISSORS: Practical considerations Journal of Chemical Information and Modeling. 54: 5-15. PMID 24289274 DOI: 10.1021/Ci400264F  0.323
2014 Wang L, Titov A, McGibbon R, Liu F, Pande VS, Martínez TJ. Erratum: Corrigendum: Discovering chemistry with an ab initio nanoreactor Nature Chemistry. 7: 87-87. DOI: 10.1038/Nchem.2139  0.653
2014 Wang LP, Martinez TJ, Pande VS. Building force fields: An automatic, systematic, and reproducible approach Journal of Physical Chemistry Letters. 5: 1885-1891. DOI: 10.1021/jz500737m  0.64
2014 Sultan MM, Kiss G, Shukla D, Pande VS. Automatic selection of order parameters in the analysis of large scale molecular dynamics simulations Journal of Chemical Theory and Computation. 10: 5217-5223. DOI: 10.1021/ct500353m  0.582
2014 Parton DL, Shukla D, Zhao Y, Pande VS, Chodera JD. Toward a Global View of the Conformational Landscape of the Human Kinome Biophysical Journal. 106: 655a-656a. DOI: 10.1016/J.Bpj.2013.11.3628  0.738
2014 Pande V. Forcebalance: a Systematic, Reproducible, Statistically Driven Approach to More Accurate Molecular Dynamics Models Biophysical Journal. 106: 44a. DOI: 10.1016/J.Bpj.2013.11.320  0.362
2014 McGibbon RT, Pande VS. Accelerating the Molecular Dynamics Sampling of Mutants: A Hierarchical Bayesian Markov State Model Strategy Biophysical Journal. 106: 411a. DOI: 10.1016/J.Bpj.2013.11.2314  0.44
2014 Beauchamp K, Pande V, Das R. Inferring Structural Ensembles from Noisy Experiments and Molecular Dynamics: Correcting Force Field Bias with Bayesian Energy Landscape Tilting Biophysical Journal. 106: 406a. DOI: 10.1016/J.Bpj.2013.11.2286  0.394
2014 Wang L, Head-Gordon T, Ponder J, Ren P, Chodera J, Eastman P, Martinez TJ, Pande VS. Systematic Improvement on the Classical Molecular Model of Water Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2273  0.77
2014 Fried SD, Wang L, Boxer SG, Pande VS. Calculations of the Electric Field in Solutions and Proteins with Polarizable Force Fields Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2271  0.648
2014 Shukla D, Roux B, Pande VS. Activation Pathways of Kinases Reveal Intermediate States as Novel Targets for Drug Design Biophysical Journal. 106: 308a. DOI: 10.1016/J.Bpj.2013.11.1784  0.63
2014 Lawrenz M, Kohlhoff K, Shukla D, Bowman G, Altman R, Pande V. Investigating Ligand-Modulation of GPCR Activation Pathways Biophysical Journal. 106: 14a. DOI: 10.1016/J.Bpj.2013.11.130  0.819
2013 McGibbon RT, Pande VS. Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics. Journal of Chemical Theory and Computation. 9: 2900-6. PMID 26583974 DOI: 10.1021/Ct400132H  0.44
2013 Lindert S, Bucher D, Eastman P, Pande V, McCammon JA. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. Journal of Chemical Theory and Computation. 9: 4684-4691. PMID 24634618 DOI: 10.1021/Ct400514P  0.419
2013 Sweet JC, Nowling RJ, Cickovski T, Sweet CR, Pande VS, Izaguirre JA. Long Timestep Molecular Dynamics on the Graphical Processing Unit. Journal of Chemical Theory and Computation. 9: 3267-3281. PMID 24436689 DOI: 10.1021/Ct400331R  0.435
2013 Wagoner JA, Pande VS. Finite domain simulations with adaptive boundaries: Accurate potentials and nonequilibrium movesets Journal of Chemical Physics. 139. PMID 24359359 DOI: 10.1063/1.4848655  0.355
2013 Lane TJ, Pande VS. Inferring the rate-length law of protein folding Plos One. 8. PMID 24339865 DOI: 10.1371/Journal.Pone.0078606  0.352
2013 Fried SD, Wang LP, Boxer SG, Ren P, Pande VS. Calculations of the electric fields in liquid solutions. The Journal of Physical Chemistry. B. 117: 16236-48. PMID 24304155 DOI: 10.1021/Jp410720Y  0.65
2013 Lane TJ, Schwantes CR, Beauchamp KA, Pande VS. Probing the origins of two-state folding Journal of Chemical Physics. 139. PMID 24116650 DOI: 10.1063/1.4823502  0.373
2013 Weber JK, Pande VS. Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing. The Journal of Chemical Physics. 139: 121917. PMID 24089729 DOI: 10.1063/1.4816633  0.457
2013 Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/Jp403802C  0.766
2013 Schwantes CR, Pande VS. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. Journal of Chemical Theory and Computation. 9: 2000-2009. PMID 23750122 DOI: 10.1021/Ct300878A  0.451
2013 Weber JK, Pande VS. Functional understanding of solvent structure in GroEL cavity through dipole field analysis. The Journal of Chemical Physics. 138: 165101. PMID 23635172 DOI: 10.1063/1.4801942  0.388
2013 Chang HW, Bacallado S, Pande VS, Carlsson GE. Persistent Topology and Metastable State in Conformational Dynamics Plos One. 8. PMID 23565139 DOI: 10.1371/Journal.Pone.0058699  0.38
2013 Weber JK, Jack RL, Pande VS. Emergence of glass-like behavior in Markov state models of protein folding dynamics. Journal of the American Chemical Society. 135: 5501-4. PMID 23540906 DOI: 10.1021/Ja4002663  0.428
2013 Weber JK, Pande VS. Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions. The Journal of Chemical Physics. 138: 085103. PMID 23464179 DOI: 10.1063/1.4792638  0.356
2013 Kiss G, Pande VS, Houk KN. Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins Methods in Enzymology. 523: 145-170. PMID 23422429 DOI: 10.1016/B978-0-12-394292-0.00007-2  0.418
2013 Gu C, Chang HW, Maibaum L, Pande VS, Carlsson GE, Guibas LJ. Building Markov state models with solvent dynamics Bmc Bioinformatics. 14. PMID 23368418 DOI: 10.1186/1471-2105-14-S2-S8  0.746
2013 Cronkite-Ratcliff B, Pande V. MSMExplorer: Visualizing Markov state models for biomolecule folding simulations Bioinformatics. 29: 950-952. PMID 23365411 DOI: 10.1093/Bioinformatics/Btt051  0.387
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, ... Pande VS, et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. 9: 461-469. PMID 23316124 DOI: 10.1021/Ct300857J  0.797
2013 Lane TJ, Shukla D, Beauchamp KA, Pande VS. To milliseconds and beyond: Challenges in the simulation of protein folding Current Opinion in Structural Biology. 23: 58-65. PMID 23237705 DOI: 10.1016/J.Sbi.2012.11.002  0.697
2013 Kohlhoff KJ, Pande VS, Altman RB. K-means for parallel architectures using all-prefix-sum sorting and updating steps Ieee Transactions On Parallel and Distributed Systems. 24: 1602-1612. DOI: 10.1109/Tpds.2012.234  0.784
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, ... Pande VS, et al. OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation Journal of Chemical Theory and Computation. 9: 461-469. DOI: 10.1021/ct300857j  0.804
2012 Lane TJ, Pande VS. Eigenvalues of the homogeneous finite linear one step master equation: Applications to downhill folding Journal of Chemical Physics. 137. PMID 23231265 DOI: 10.1063/1.4769295  0.371
2012 Wagoner JA, Pande VS. Reducing the effect of Metropolization on mixing times in molecular dynamics simulations Journal of Chemical Physics. 137. PMID 23231215 DOI: 10.1063/1.4769301  0.399
2012 Ring AM, Lin JX, Feng D, Mitra S, Rickert M, Bowman GR, Pande VS, Li P, Moraga I, Spolski R, Ozkan E, Leonard WJ, Garcia KC. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nature Immunology. 13: 1187-95. PMID 23104097 DOI: 10.1038/Ni.2449  0.518
2012 Beauchamp KA, McGibbon R, Lin YS, Pande VS. Simple few-state models reveal hidden complexity in protein folding Proceedings of the National Academy of Sciences of the United States of America. 109: 17807-17813. PMID 22778442 DOI: 10.1073/Pnas.1201810109  0.486
2012 Beauchamp KA, Lin YS, Das R, Pande VS. Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements. Journal of Chemical Theory and Computation. 8: 1409-1414. PMID 22754404 DOI: 10.1021/Ct2007814  0.348
2012 Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. Journal of the American Chemical Society. 134: 12565-77. PMID 22747188 DOI: 10.1021/Ja302528Z  0.793
2012 Lane TJ, Pande VS. A simple model predicts experimental folding rates and a hub-like topology. The Journal of Physical Chemistry. B. 116: 6764-74. PMID 22452581 DOI: 10.1021/Jp212332C  0.443
2012 Levin AM, Bates DL, Ring AM, Krieg C, Lin JT, Su L, Moraga I, Raeber ME, Bowman GR, Novick P, Pande VS, Fathman CG, Boyman O, Garcia KC. Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature. 484: 529-33. PMID 22446627 DOI: 10.1038/Nature10975  0.531
2012 Novick PA, Lopes DH, Branson KM, Esteras-Chopo A, Graef IA, Bitan G, Pande VS. Design of β-amyloid aggregation inhibitors from a predicted structural motif. Journal of Medicinal Chemistry. 55: 3002-10. PMID 22420626 DOI: 10.1021/Jm201332P  0.338
2012 Weber JK, Pande VS. Protein folding is mechanistically robust Biophysical Journal. 102: 859-867. PMID 22385857 DOI: 10.1016/J.Bpj.2012.01.028  0.445
2012 Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer Biophysical Journal. 102: 315-324. PMID 22339868 DOI: 10.1016/J.Bpj.2011.12.002  0.618
2012 Brandman R, Brandman Y, Pande VS. Sequence coevolution between RNA and protein characterized by mutual information between residue triplets. Plos One. 7: e30022. PMID 22279560 DOI: 10.1371/Journal.Pone.0030022  0.304
2012 Brandman R, Brandman Y, Pande VS. A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome. Plos One. 7: e29377. PMID 22235290 DOI: 10.1371/Journal.Pone.0029377  0.372
2012 Voelz VA, Pande VS. Calculation of rate spectra from noisy time series data Proteins: Structure, Function and Bioinformatics. 80: 342-351. PMID 22095854 DOI: 10.1002/Prot.23171  0.642
2012 Delp SL, Ku JP, Pande VS, Sherman MA, Altman RB. Simbios: an NIH national center for physics-based simulation of biological structures. Journal of the American Medical Informatics Association : Jamia. 19: 186-9. PMID 22081222 DOI: 10.1136/Amiajnl-2011-000488  0.542
2012 Chodera JD, Pande VS. Erratum: Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments [Phys. Rev. Lett.107, 098102 (2011)] Physical Review Letters. 108. DOI: 10.1103/Physrevlett.108.249901  0.54
2012 Fenn T, Schnieders M, Pande V. Bayesian Modeling of Crystallographic Disorder Biophysical Journal. 102: 225a. DOI: 10.1016/J.Bpj.2011.11.1235  0.353
2011 Schnieders MJ, Fenn TD, Pande VS. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals. Journal of Chemical Theory and Computation. 7: 1141-1156. PMID 26606362 DOI: 10.1021/Ct100506D  0.326
2011 Weber JK, Pande VS. Characterization and rapid sampling of protein folding Markov state model topologies. Journal of Chemical Theory and Computation. 7: 3405-3411. PMID 22140370 DOI: 10.1021/Ct2004484  0.413
2011 Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. Journal of Chemical Theory and Computation. 7: 3412-3419. PMID 22125474 DOI: 10.1021/Ct200463M  0.803
2011 Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. Markov State model reveals folding and functional dynamics in ultra-long MD trajectories Journal of the American Chemical Society. 133: 18413-18419. PMID 21988563 DOI: 10.1021/Ja207470H  0.78
2011 Chodera JD, Pande VS. Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. Physical Review Letters. 107: 098102. PMID 21929272 DOI: 10.1103/Physrevlett.107.098102  0.584
2011 Pande VS. (Compressed) sensing and sensibility Proceedings of the National Academy of Sciences of the United States of America. 108: 14713-14714. PMID 21873202 DOI: 10.1073/Pnas.1111659108  0.352
2011 Chodera JD, Pande VS. The social network (of protein conformations). Proceedings of the National Academy of Sciences of the United States of America. 108: 12969-70. PMID 21804033 DOI: 10.1073/Pnas.1109571108  0.599
2011 Rajadas J, Liu CW, Novick P, Kelley NW, Inayathullah M, Lemieux MC, Pande VS. Rationally designed turn promoting mutation in the amyloid-β peptide sequence stabilizes oligomers in solution. Plos One. 6: e21776. PMID 21799748 DOI: 10.1371/Journal.Pone.0021776  0.303
2011 Beauchamp KA, Ensign DL, Das R, Pande VS. Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments Proceedings of the National Academy of Sciences of the United States of America. 108: 12734-12739. PMID 21768345 DOI: 10.1073/Pnas.1010880108  0.444
2011 Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. The Journal of Chemical Physics. 134: 244108. PMID 21721613 DOI: 10.1063/1.3592153  0.807
2011 Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. The Journal of Chemical Physics. 134: 244107. PMID 21721612 DOI: 10.1063/1.3592152  0.814
2011 Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman RB. CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. Bioinformatics (Oxford, England). 27: 2322-3. PMID 21712246 DOI: 10.1093/Bioinformatics/Btr386  0.77
2011 Wagoner JA, Pande VS. A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent Journal of Chemical Physics. 134. PMID 21663340 DOI: 10.1063/1.3595262  0.387
2011 Fenn TD, Schnieders MJ, Mustyakimov M, Wu C, Langan P, Pande VS, Brunger AT. Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration. Structure (London, England : 1993). 19: 523-33. PMID 21481775 DOI: 10.1016/J.Str.2011.01.015  0.513
2011 Kasson PM, Pande VS. A bundling of viral fusion mechanisms. Proceedings of the National Academy of Sciences of the United States of America. 108: 3827-8. PMID 21368165 DOI: 10.1073/Pnas.1101072108  0.589
2011 Kasson PM, Lindahl E, Pande VS. Water ordering at membrane interfaces controls fusion dynamics. Journal of the American Chemical Society. 133: 3812-5. PMID 21351772 DOI: 10.1021/Ja200310D  0.61
2011 Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology. 21: 150-60. PMID 21349700 DOI: 10.1016/J.Sbi.2011.01.011  0.706
2011 Bowman GR, Voelz VA, Pande VS. Atomistic folding simulations of the five-helix bundle protein λ 6-85 Journal of the American Chemical Society. 133: 664-667. PMID 21174461 DOI: 10.1021/Ja106936N  0.795
2011 Stumpe MC, Blinov N, Wishart D, Kovalenko A, Pande VS. Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation. The Journal of Physical Chemistry. B. 115: 319-28. PMID 21174421 DOI: 10.1021/Jp102587Q  0.404
2011 Bowman GR, Voelz VA, Pande VS. Taming the complexity of protein folding Current Opinion in Structural Biology. 21: 4-11. PMID 21081274 DOI: 10.1016/J.Sbi.2010.10.006  0.765
2011 Pronk S, Larsson P, Pouya I, Bowman GR, Haque IS, Beauchamp K, Hess B, Pande VS, Kasson PM, Lindahl E. Copernicus: A new paradigm for parallel adaptive molecular dynamics Proceedings of 2011 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis. DOI: 10.1145/2063384.2063465  0.741
2011 Chodera JD, Pande VS. Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments Physical Review Letters. 107. DOI: 10.1103/PhysRevLett.107.098102  0.486
2011 Kohlhoff KJ, Sosnick MH, Hsu WT, Pande VS, Altman RB. CAMPAIGN: An open-source library of GPU-accelerated data clustering algorithms Bioinformatics. 27: 2322-2323. DOI: 10.1093/bioinformatics/btr386  0.75
2011 Chodera JD, Pande VS. The social network (of protein conformations) Proceedings of the National Academy of Sciences of the United States of America. 108: 12969-12970. DOI: 10.1073/pnas.1109571108  0.508
2011 Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. MSMBuilder2: Modeling conformational dynamics on the picosecond to millisecond scale Journal of Chemical Theory and Computation. 7: 3412-3419. DOI: 10.1021/ct200463m  0.581
2011 Voelz VA, Jäger M, Zhu L, Yao S, Bakajin O, Weiss S, Lapidus LJ, Pande VS. Markov State Models of Millisecond Folder ACBP Reveals New Views of the Folding Reaction Biophysical Journal. 100: 515a. DOI: 10.1016/J.Bpj.2010.12.3015  0.714
2011 Zhu L, Voelz VA, Bakajin O, Pande VS, Lapidus LJ. Revealing the Early Events of ACBP Folding by Ultrarapid Mixing Biophysical Journal. 100: 396a. DOI: 10.1016/J.Bpj.2010.12.2353  0.697
2011 Chen Y, Voelz VA, Bakajin O, Pande VS, Lapidus LJ. Diffusion of Unfolded Acyl-Coenzyme A-Binding Protein Over a Complete Range of Denaturant Biophysical Journal. 100: 211a. DOI: 10.1016/J.Bpj.2010.12.1362  0.678
2010 Bowman GR, Ensign DL, Pande VS. Enhanced modeling via network theory: Adaptive sampling of Markov state models. Journal of Chemical Theory and Computation. 6: 787-794. PMID 23626502 DOI: 10.1021/Ct900620B  0.659
2010 Pande VS. Simple theory of protein folding kinetics. Physical Review Letters. 105: 198101. PMID 21231198 DOI: 10.1103/Physrevlett.105.198101  0.463
2010 Lucent D, Snow CD, Aitken CE, Pande VS. Non-bulk-like solvent behavior in the ribosome exit tunnel Plos Computational Biology. 6. PMID 20975935 DOI: 10.1371/Journal.Pcbi.1000963  0.698
2010 Ensign DL, Pande VS. Bayesian inference for Brownian dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 82: 016705. PMID 20866759 DOI: 10.1103/Physreve.82.016705  0.301
2010 Kasson PM, Lindahl E, Pande VS. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails. Plos Computational Biology. 6: e1000829. PMID 20585620 DOI: 10.1371/Journal.Pcbi.1000829  0.658
2010 Pande VS, Beauchamp K, Bowman GR. Everything you wanted to know about Markov State Models but were afraid to ask. Methods (San Diego, Calif.). 52: 99-105. PMID 20570730 DOI: 10.1016/J.Ymeth.2010.06.002  0.67
2010 Eastman P, Pande VS. CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations. Journal of Chemical Theory and Computation. 6: 434-437. PMID 20563234 DOI: 10.1021/Ct900463W  0.374
2010 Fenn TD, Schnieders MJ, Brunger AT, Pande VS. Polarizable atomic multipole x-ray refinement: hydration geometry and application to macromolecules. Biophysical Journal. 98: 2984-92. PMID 20550911 DOI: 10.1016/J.Bpj.2010.02.057  0.552
2010 Bowman GR, Pande VS. Protein folded states are kinetic hubs. Proceedings of the National Academy of Sciences of the United States of America. 107: 10890-5. PMID 20534497 DOI: 10.1073/Pnas.1003962107  0.675
2010 England JL, Pande VS. Charge, hydrophobicity, and confined water: putting past simulations into a simple theoretical framework. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 88: 359-69. PMID 20453936 DOI: 10.1139/o09-187  0.657
2010 Bowman GR, Huang X, Pande VS. Network models for molecular kinetics and their initial applications to human health. Cell Research. 20: 622-30. PMID 20421891 DOI: 10.1038/Cr.2010.57  0.687
2010 Voelz VA, Singh VR, Wedemeyer WJ, Lapidus LJ, Pande VS. Unfolded-state dynamics and structure of protein L characterized by simulation and experiment. Journal of the American Chemical Society. 132: 4702-9. PMID 20218718 DOI: 10.1021/Ja908369H  0.732
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D  0.703
2010 Voelz VA, Bowman GR, Beauchamp K, Pande VS. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). Journal of the American Chemical Society. 132: 1526-8. PMID 20070076 DOI: 10.1021/Ja9090353  0.808
2010 Ensign DL, Pande VS. Bayesian detection of intensity changes in single molecule and molecular dynamics trajectories. The Journal of Physical Chemistry. B. 114: 280-92. PMID 20000829 DOI: 10.1021/Jp906786B  0.355
2010 Kasson PM, Pande VS. "Cross-graining": efficient multi-scale simulation via Markov state models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 260-8. PMID 19908378  0.604
2010 Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS. Constructing multi-resolution markov state models (MSMS) to elucidate RNA hairpin folding mechanisms Pacific Symposium On Biocomputing 2010, Psb 2010. 228-239. PMID 19908375  0.682
2010 Eastman P, Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. Journal of Computational Chemistry. 31: 1268-72. PMID 19847780 DOI: 10.1002/Jcc.21413  0.398
2010 Bowman GR, Pande VS. Protein folded states are kinetic hubs (Proceedings of the National Academy of Sciences of the United States of America (2010) 107, (10890-10895) DOI: 10.1073/pnas.1003962107) Proceedings of the National Academy of Sciences of the United States of America. 107: 16749. DOI: 10.1073/pnas.1012332107  0.561
2010 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. X-Ray Crystallography Refinement as Ewald Intended: From Drug Design to Ribosome Crystals Biophysical Journal. 98: 177a. DOI: 10.1016/J.Bpj.2009.12.946  0.544
2010 Fenn T, Schnieders M, Pande V, Brunger A. Is Theory Leading Neutron Diffraction in Macromolecular Solvent Networks? Biophysical Journal. 98: 760a. DOI: 10.1016/J.Bpj.2009.12.4172  0.545
2010 Kasson P, Lindahl E, Pande V. Atomic-Resolution Simulations Yield New Insight into Vesicle Fusion and Fusion Protein Mechanisms Biophysical Journal. 98: 616a. DOI: 10.1016/J.Bpj.2009.12.3363  0.646
2010 Bowman GR, Pande VS. Millisecond Timescale, Atomistic Protein Folding Simulations Yield a Network Theory for Protein Folding Biophysical Journal. 98: 614a. DOI: 10.1016/J.Bpj.2009.12.3352  0.694
2010 Lapidus LJ, Chen Y, Singh VR, Waldauer SA, Buscarino E, Voelz VA, Pande VS. Connecting Unfolded Protein Dynamics and Aggregation Biophysical Journal. 98: 257a. DOI: 10.1016/J.Bpj.2009.12.1396  0.422
2010 Pande V. Computational Nanomedicine: Simulating Protein Misfolding Disease Biophysical Journal. 98: 223a. DOI: 10.1016/J.Bpj.2009.12.1207  0.411
2009 Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? Rna (New York, N.Y.). 15: 2195-205. PMID 19850914 DOI: 10.1261/Rna.1747509  0.335
2009 Huang X, Bowman GR, Bacallado S, Pande VS. Rapid equilibrium sampling initiated from nonequilibrium data. Proceedings of the National Academy of Sciences of the United States of America. 106: 19765-9. PMID 19805023 DOI: 10.1073/Pnas.0909088106  0.7
2009 Bowman GR, Beauchamp KA, Boxer G, Pande VS. Progress and challenges in the automated construction of Markov state models for full protein systems. The Journal of Chemical Physics. 131: 124101. PMID 19791846 DOI: 10.1063/1.3216567  0.684
2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 77: 66-80. PMID 19714776 DOI: 10.1002/Prot.22538  0.549
2009 Schnieders MJ, Fenn TD, Pande VS, Brunger AT. Polarizable atomic multipole X-ray refinement: application to peptide crystals. Acta Crystallographica. Section D, Biological Crystallography. 65: 952-65. PMID 19690373 DOI: 10.1107/S0907444909022707  0.542
2009 Ensign DL, Pande VS. Bayesian single-exponential kinetics in single-molecule experiments and simulations. The Journal of Physical Chemistry. B. 113: 12410-23. PMID 19681587 DOI: 10.1021/Jp903107C  0.414
2009 Bacallado S, Chodera JD, Pande V. Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. The Journal of Chemical Physics. 131: 045106. PMID 19655927 DOI: 10.1063/1.3192309  0.67
2009 Kasson PM, Ensign DL, Pande VS. Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin. Journal of the American Chemical Society. 131: 11338-40. PMID 19637916 DOI: 10.1021/Ja904557W  0.603
2009 Bowman GR, Pande VS. The roles of entropy and kinetics in structure prediction. Plos One. 4: e5840. PMID 19513117 DOI: 10.1371/Journal.Pone.0005840  0.633
2009 Bowman GR, Huang X, Pande VS. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (San Diego, Calif.). 49: 197-201. PMID 19410002 DOI: 10.1016/J.Ymeth.2009.04.013  0.713
2009 Voelz VA, Luttmann E, Bowman GR, Pande VS. Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. International Journal of Molecular Sciences. 10: 1013-30. PMID 19399235 DOI: 10.3390/Ijms10031013  0.761
2009 Ensign DL, Pande VS. The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations. Biophysical Journal. 96: L53-5. PMID 19383445 DOI: 10.1016/J.Bpj.2009.01.024  0.478
2009 Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, Carlsson G. Topological methods for exploring low-density states in biomolecular folding pathways. The Journal of Chemical Physics. 130: 144115. PMID 19368437 DOI: 10.1063/1.3103496  0.708
2009 Kelley NW, Huang X, Tam S, Spiess C, Frydman J, Pande VS. The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation. Journal of Molecular Biology. 388: 919-27. PMID 19361448 DOI: 10.1016/J.Jmb.2009.01.032  0.553
2009 Kasson PM, Pande VS. Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 492-503. PMID 19209725  0.527
2009 Voelz VA, Petrone P, Pande VS. A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 340-52. PMID 19209713  0.639
2009 Lucent D, England J, Pande V. Inside the chaperonin toolbox: theoretical and computational models for chaperonin mechanism. Physical Biology. 6: 015003. PMID 19208937 DOI: 10.1088/1478-3975/6/1/015003  0.7
2009 Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, Legrand S, Beberg AL, Ensign DL, Bruns CM, Pande VS. Accelerating molecular dynamic simulation on graphics processing units. Journal of Computational Chemistry. 30: 864-72. PMID 19191337 DOI: 10.1002/Jcc.21209  0.388
2009 Chong LT, Pitera JW, Swope WC, Pande VS. Comparison of computational approaches for predicting the effects of missense mutations on p53 function. Journal of Molecular Graphics & Modelling. 27: 978-82. PMID 19168381 DOI: 10.1016/J.Jmgm.2008.12.006  0.781
2009 Bowman GR, Pande VS. Simulated tempering yields insight into the low-resolution Rosetta scoring functions. Proteins. 74: 777-88. PMID 18767152 DOI: 10.1002/Prot.22210  0.64
2009 Luttmann E, Ensign DL, Vaidyanathan V, Houston M, Rimon N, Øland J, Jayachandran G, Friedrichs M, Pande VS. Accelerating molecular dynamic simulation on the cell processor and Playstation 3. Journal of Computational Chemistry. 30: 268-74. PMID 18615421 DOI: 10.1002/Jcc.21054  0.748
2009 Beberg AL, Ensign DL, Jayachandran G, Khaliq S, Pande VS. Folding@home: Lessons from eight years of volunteer distributed computing Ipdps 2009 - Proceedings of the 2009 Ieee International Parallel and Distributed Processing Symposium. DOI: 10.1109/IPDPS.2009.5160922  0.689
2009 Graef I, Alhamadsheh MM, Esteras-Chopo A, Branson K, Bose M, Pande V. Breaking protein-protein interactions: A combined chemical and computational approach to develop a new class of protein aggregation inhibitors Alzheimers & Dementia. 5. DOI: 10.1016/J.Jalz.2009.04.966  0.327
2009 Bowman GR, Huang X, Pande VS. Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales Biophysical Journal. 96: 575a. DOI: 10.1016/J.Bpj.2008.12.3002  0.736
2009 Kasson P, Pande V. Analysis Of Influenza Hemagglutinin Ligand-binding From Mutational Data And Molecular Motion Biophysical Journal. 96: 420a. DOI: 10.1016/J.Bpj.2008.12.2150  0.619
2008 Schmidt JP, Delp SL, Sherman MA, Taylor CA, Pande VS, Altman RB. The Simbios National Center: Systems Biology in Motion. Proceedings of the Ieee. Institute of Electrical and Electronics Engineers. 96: 1266. PMID 20107615 DOI: 10.1109/JPROC.2008.925454  0.426
2008 Kelley NW, Vishal V, Krafft GA, Pande VS. Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach. The Journal of Chemical Physics. 129: 214707. PMID 19063575 DOI: 10.1063/1.3010881  0.723
2008 Petrone PM, Snow CD, Lucent D, Pande VS. Side-chain recognition and gating in the ribosome exit tunnel. Proceedings of the National Academy of Sciences of the United States of America. 105: 16549-54. PMID 18946046 DOI: 10.1073/Pnas.0801795105  0.806
2008 Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society. 130: 12334-41. PMID 18722445 DOI: 10.1021/Ja800854U  0.361
2008 England JL, Lucent D, Pande VS. A role for confined water in chaperonin function. Journal of the American Chemical Society. 130: 11838-9. PMID 18710231 DOI: 10.1021/Ja802248M  0.709
2008 England JL, Pande VS, Haran G. Chemical denaturants inhibit the onset of dewetting. Journal of the American Chemical Society. 130: 11854-5. PMID 18707183 DOI: 10.1021/Ja803972G  0.696
2008 Kasson PM, Pande VS. Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin. Biophysical Journal. 95: L48-50. PMID 18641068 DOI: 10.1529/Biophysj.108.141507  0.6
2008 England JL, Pande VS. Potential for modulation of the hydrophobic effect inside chaperonins. Biophysical Journal. 95: 3391-9. PMID 18599630 DOI: 10.1529/Biophysj.108.131037  0.707
2008 Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS. Structural insight into RNA hairpin folding intermediates. Journal of the American Chemical Society. 130: 9676-8. PMID 18593120 DOI: 10.1021/Ja8032857  0.711
2008 Huang X, Bowman GR, Pande VS. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. The Journal of Chemical Physics. 128: 205106. PMID 18513049 DOI: 10.1063/1.2908251  0.697
2008 Sweet CR, Petrone P, Pande VS, Izaguirre JA. Normal mode partitioning of Langevin dynamics for biomolecules. The Journal of Chemical Physics. 128: 145101. PMID 18412479 DOI: 10.1063/1.2883966  0.734
2008 Monticelli L, Sorin EJ, Tieleman DP, Pande VS, Colombo G. Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories. Journal of Computational Chemistry. 29: 1740-52. PMID 18307167 DOI: 10.1002/Jcc.20935  0.779
2008 England J, Lucent D, Pande V. Rattling the cage: computational models of chaperonin-mediated protein folding. Current Opinion in Structural Biology. 18: 163-9. PMID 18291636 DOI: 10.1016/J.Sbi.2007.12.013  0.724
2008 England JL, Park S, Pande VS. Theory for an order-driven disruption of the liquid state in water. The Journal of Chemical Physics. 128: 044503. PMID 18247965 DOI: 10.1063/1.2823129  0.686
2008 Rother D, Sapiro G, Pande V. Statistical characterization of protein ensembles. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 42-55. PMID 18245874 DOI: 10.1109/Tcbb.2007.1061  0.434
2008 Rhee YM, Pande VS. Solvent viscosity dependence of the protein folding dynamics. The Journal of Physical Chemistry. B. 112: 6221-7. PMID 18229911 DOI: 10.1021/Jp076301D  0.703
2008 Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. Journal of Medicinal Chemistry. 51: 769-79. PMID 18215013 DOI: 10.1021/Jm070549+  0.601
2008 Robertson A, Luttmann E, Pande VS. Effects of long-range electrostatic forces on simulated protein folding kinetics. Journal of Computational Chemistry. 29: 694-700. PMID 17849394 DOI: 10.1002/Jcc.20828  0.443
2008 Shirts MR, Pande VS. Erratum: “Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration” [J. Chem. Phys. 122, 144107 (2005)] The Journal of Chemical Physics. 129: 229901. DOI: 10.1063/1.3033406  0.601
2008 Ensign DL, Kasson PM, Pande VS. Addendum to “Heterogeneity Even at the Speed Limit of Folding: Large-Scale Molecular Dynamics Study of a Fast-Folding Variant of the Villin Headpiece” [J. Mol. Biol. 374 (2007) 806–816] Journal of Molecular Biology. 383: 935. DOI: 10.1016/J.Jmb.2008.07.066  0.644
2008 Kasson PM, Pande VS. Simulating mechanisms for control of vesicle fusion Aiche Annual Meeting, Conference Proceedings.  0.573
2007 Kasson PM, Pande VS. Control of membrane fusion mechanism by lipid composition: predictions from ensemble molecular dynamics. Plos Computational Biology. 3: e220. PMID 18020701 DOI: 10.1371/Journal.Pcbi.0030220  0.617
2007 Kasson PM, Pande VS. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 40-50. PMID 17992744  0.579
2007 Ensign DL, Kasson PM, Pande VS. Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. Journal of Molecular Biology. 374: 806-16. PMID 17950314 DOI: 10.1016/J.Jmb.2007.09.069  0.714
2007 Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. The Journal of Physical Chemistry. B. 111: 13052-63. PMID 17949030 DOI: 10.1021/Jp0735987  0.764
2007 Park S, Klein TE, Pande VS. Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations. Biophysical Journal. 93: 4108-15. PMID 17766343 DOI: 10.1529/Biophysj.107.108100  0.426
2007 Park S, Pande VS. Choosing weights for simulated tempering. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 016703. PMID 17677590 DOI: 10.1103/Physreve.76.016703  0.394
2007 Hinrichs NS, Pande VS. Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. The Journal of Chemical Physics. 126: 244101. PMID 17614531 DOI: 10.1063/1.2740261  0.823
2007 Lucent D, Vishal V, Pande VS. Protein folding under confinement: a role for solvent. Proceedings of the National Academy of Sciences of the United States of America. 104: 10430-4. PMID 17563390 DOI: 10.1073/Pnas.0608256104  0.726
2007 Kasson PM, Zomorodian A, Park S, Singhal N, Guibas LJ, Pande VS. Persistent voids: a new structural metric for membrane fusion. Bioinformatics (Oxford, England). 23: 1753-9. PMID 17488753 DOI: 10.1093/Bioinformatics/Btm250  0.624
2007 Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. The Journal of Chemical Physics. 126: 155101. PMID 17461665 DOI: 10.1063/1.2714538  0.828
2007 Jayachandran G, Vishal V, García AE, Pande VS. Local structure formation in simulations of two small proteins. Journal of Structural Biology. 157: 491-9. PMID 17098444 DOI: 10.1016/J.Jsb.2006.10.001  0.825
2006 Jayachandran G, Shirts MR, Park S, Pande VS. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. The Journal of Chemical Physics. 125: 084901. PMID 16965051 DOI: 10.1063/1.2221680  0.794
2006 Zagrovic B, Pande VS. Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide-angle solution X-ray scattering profiles. Journal of the American Chemical Society. 128: 11742-3. PMID 16953598 DOI: 10.1021/Ja0640694  0.632
2006 Kasson PM, Kelley NW, Singhal N, Vrljic M, Brunger AT, Pande VS. Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proceedings of the National Academy of Sciences of the United States of America. 103: 11916-21. PMID 16880392 DOI: 10.1073/Pnas.0601597103  0.737
2006 Suydam IT, Snow CD, Pande VS, Boxer SG. Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science (New York, N.Y.). 313: 200-4. PMID 16840693 DOI: 10.1126/Science.1127159  0.649
2006 Sorin EJ, Pande VS. Nanotube confinement denatures protein helices. Journal of the American Chemical Society. 128: 6316-7. PMID 16683786 DOI: 10.1021/Ja060917J  0.729
2006 Jayachandran G, Vishal V, Pande VS. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece. The Journal of Chemical Physics. 124: 164902. PMID 16674165 DOI: 10.1063/1.2186317  0.842
2006 Snow CD, Rhee YM, Pande VS. Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophysical Journal. 91: 14-24. PMID 16617068 DOI: 10.1529/Biophysj.105.075689  0.792
2006 Park S, Pande VS. Validation of Markov state models using Shannon's entropy. The Journal of Chemical Physics. 124: 054118. PMID 16468862 DOI: 10.1063/1.2166393  0.387
2006 Chong LT, Swope WC, Pitera JW, Pande VS. Kinetic computational alanine scanning: application to p53 oligomerization. Journal of Molecular Biology. 357: 1039-49. PMID 16457841 DOI: 10.1016/J.Jmb.2005.12.083  0.794
2006 Sorin EJ, Rhee YM, Shirts MR, Pande VS. The solvation interface is a determining factor in peptide conformational preferences. Journal of Molecular Biology. 356: 248-56. PMID 16364361 DOI: 10.1016/J.Jmb.2005.11.058  0.799
2006 Petrone P, Pande VS. Can conformational change be described by only a few normal modes? Biophysical Journal. 90: 1583-1593. PMID 16361336 DOI: 10.1529/Biophysj.105.070045  0.721
2006 Elsen E, Houston M, Vishal V, Darve E, Hanrahan P, Pande V. N-Body simulation on GPUs Proceedings of the 2006 Acm/Ieee Conference On Supercomputing, Sc'06. DOI: 10.1145/1188455.1188649  0.643
2006 Rhee YM, Pande VS. On the role of chemical detail in simulating protein folding kinetics Chemical Physics. 323: 66-77. DOI: 10.1016/J.Chemphys.2005.08.060  0.716
2005 Rhee YM, Pande VS. One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. The Journal of Physical Chemistry. B. 109: 6780-6. PMID 16851763 DOI: 10.1021/Jp045544S  0.626
2005 Elmer SP, Park S, Pande VS. Foldamer dynamics expressed via Markov state models. II. State space decomposition. The Journal of Chemical Physics. 123: 114903. PMID 16392593 DOI: 10.1063/1.2008230  0.792
2005 Elmer SP, Park S, Pande VS. Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water. The Journal of Chemical Physics. 123: 114902. PMID 16392592 DOI: 10.1063/1.2001648  0.818
2005 Singhal N, Pande VS. Error analysis and efficient sampling in Markovian state models for molecular dynamics. The Journal of Chemical Physics. 123: 204909. PMID 16351319 DOI: 10.1063/1.2116947  0.373
2005 Zagrovic B, Jayachandran G, Millett IS, Doniach S, Pande VS. How large is an alpha-helix? Studies of the radii of gyration of helical peptides by small-angle X-ray scattering and molecular dynamics. Journal of Molecular Biology. 353: 232-41. PMID 16171817 DOI: 10.1016/J.Jmb.2005.08.053  0.795
2005 Park S, Radmer RJ, Klein TE, Pande VS. A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides. Journal of Computational Chemistry. 26: 1612-6. PMID 16170799 DOI: 10.1002/Jcc.20301  0.377
2005 Fujitani H, Tanida Y, Ito M, Jayachandran G, Snow CD, Shirts MR, Sorin EJ, Pande VS. Direct calculation of the binding free energies of FKBP ligands. The Journal of Chemical Physics. 123: 084108. PMID 16164283 DOI: 10.1063/1.1999637  0.78
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  0.824
2005 Snow CD, Sorin EJ, Rhee YM, Pande VS. How well can simulation predict protein folding kinetics and thermodynamics? Annual Review of Biophysics and Biomolecular Structure. 34: 43-69. PMID 15869383 DOI: 10.1146/Annurev.Biophys.34.040204.144447  0.828
2005 Shirts MR, Pande VS. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. The Journal of Chemical Physics. 122: 144107. PMID 15847516 DOI: 10.1063/1.1873592  0.642
2005 Shirts MR, Pande VS. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. The Journal of Chemical Physics. 122: 134508. PMID 15847482 DOI: 10.1063/1.1877132  0.662
2005 Elmer SP, Pande VS. Length dependent folding kinetics of phenylacetylene oligomers: structural characterization of a kinetic trap. The Journal of Chemical Physics. 122: 124908. PMID 15836425 DOI: 10.1063/1.1867375  0.826
2005 Sorin EJ, Pande VS. Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. Journal of Computational Chemistry. 26: 682-90. PMID 15754305 DOI: 10.1002/Jcc.20208  0.743
2005 Sorin EJ, Rhee YM, Pande VS. Does water play a structural role in the folding of small nucleic acids? Biophysical Journal. 88: 2516-24. PMID 15681648 DOI: 10.1529/Biophysj.104.055087  0.831
2005 Sorin EJ, Pande VS. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal. 88: 2472-93. PMID 15665128 DOI: 10.1529/Biophysj.104.051938  0.796
2005 Chong LT, Snow CD, Rhee YM, Pande VS. Dimerization of the p53 oligomerization domain: identification of a folding nucleus by molecular dynamics simulations. Journal of Molecular Biology. 345: 869-78. PMID 15588832 DOI: 10.1016/J.Jmb.2004.10.083  0.834
2005 Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW. Erratum: Random-coil behavior and the dimensions of chemically unfolded proteins (Proceedings of The National Academy of Sciences of The United States of America (August 24, 2004) 101, 34 (12491-12496)) Proceedings of the National Academy of Sciences of the United States of America. 102. DOI: 10.1073/Pnas.0507472102  0.314
2004 Elmer SP, Pande VS. Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers. The Journal of Chemical Physics. 121: 12760-71. PMID 15606301 DOI: 10.1063/1.1812272  0.821
2004 Zagrovic B, Pande VS. How does averaging affect protein structure comparison on the ensemble level? Biophysical Journal. 87: 2240-6. PMID 15454426 DOI: 10.1529/Biophysj.104.042184  0.68
2004 Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N, Dothager RS, Seifert S, Thiyagarajan P, Sosnick TR, Hasan MZ, Pande VS, Ruczinski I, Doniach S, Plaxco KW. Random-coil behavior and the dimensions of chemically unfolded proteins. Proceedings of the National Academy of Sciences of the United States of America. 101: 12491-6. PMID 15314214 DOI: 10.1073/Pnas.0403643101  0.653
2004 Lenz P, Zagrovic B, Shapiro J, Pande VS. Folding probabilities: a novel approach to folding transitions and the two-dimensional Ising-model. The Journal of Chemical Physics. 120: 6769-78. PMID 15267572 DOI: 10.1063/1.1667470  0.691
2004 Singhal N, Snow CD, Pande VS. Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. The Journal of Chemical Physics. 121: 415-25. PMID 15260562 DOI: 10.1063/1.1738647  0.712
2004 Kasson PM, Pande VS. Molecular dynamics simulation of lipid reorientation at bilayer edges. Biophysical Journal. 86: 3744-9. PMID 15189870 DOI: 10.1529/Biophysj.103.029652  0.639
2004 Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS. Simulations of the role of water in the protein-folding mechanism. Proceedings of the National Academy of Sciences of the United States of America. 101: 6456-61. PMID 15090647 DOI: 10.1073/Pnas.0307898101  0.822
2004 Sorin EJ, Nakatani BJ, Rhee YM, Jayachandran G, Vishal V, Pande VS. Does native state topology determine the RNA folding mechanism? Journal of Molecular Biology. 337: 789-97. PMID 15033351 DOI: 10.1016/J.Jmb.2004.02.024  0.829
2004 Snow CD, Qiu L, Du D, Gai F, Hagen SJ, Pande VS. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 101: 4077-82. PMID 15020773 DOI: 10.1073/Pnas.0305260101  0.744
2003 Shirts MR, Bair E, Hooker G, Pande VS. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. Physical Review Letters. 91: 140601. PMID 14611511 DOI: 10.1103/Physrevlett.91.140601  0.587
2003 Zagrovic B, Pande VS. Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties. Nature Structural Biology. 10: 955-61. PMID 14555998 DOI: 10.1038/Nsb995  0.675
2003 Larson SM, Pande VS. Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein. Journal of Molecular Biology. 332: 275-86. PMID 12946364 DOI: 10.1016/S0022-2836(03)00832-5  0.643
2003 Sorin EJ, Rhee YM, Nakatani BJ, Pande VS. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophysical Journal. 85: 790-803. PMID 12885628 DOI: 10.1016/S0006-3495(03)74520-2  0.843
2003 Zagrovic B, Pande V. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. Journal of Computational Chemistry. 24: 1432-6. PMID 12868108 DOI: 10.1002/Jcc.10297  0.668
2003 Larson SM, Garg A, Desjarlais JR, Pande VS. Increased detection of structural templates using alignments of designed sequences. Proteins. 51: 390-6. PMID 12696050 DOI: 10.1002/Prot.10346  0.611
2003 Pande VS. Meeting halfway on the bridge between protein folding theory and experiment. Proceedings of the National Academy of Sciences of the United States of America. 100: 3555-6. PMID 12657736 DOI: 10.1073/Pnas.0830965100  0.424
2003 Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, Larson SM, Rhee YM, Shirts MR, Snow CD, Sorin EJ, Zagrovic B. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers. 68: 91-109. PMID 12579582 DOI: 10.1002/Bip.10219  0.823
2003 Rhee YM, Pande VS. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophysical Journal. 84: 775-86. PMID 12547762 DOI: 10.1016/S0006-3495(03)74897-8  0.697
2003 Jewett AI, Pande VS, Plaxco KW. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. Journal of Molecular Biology. 326: 247-53. PMID 12547206 DOI: 10.1016/S0022-2836(02)01356-6  0.408
2003 Shirts MR, Pitera JW, Swope WC, Pande VS. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins Journal of Chemical Physics. 119: 5740-5761. DOI: 10.1063/1.1587119  0.815
2002 Snow CD, Zagrovic B, Pande VS. The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. Journal of the American Chemical Society. 124: 14548-9. PMID 12465960 DOI: 10.1021/Ja028604L  0.818
2002 Larson SM, England JL, Desjarlais JR, Pande VS. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Science : a Publication of the Protein Society. 11: 2804-13. PMID 12441379 DOI: 10.1110/Ps.0203902  0.755
2002 Snow CD, Nguyen H, Pande VS, Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420: 102-6. PMID 12422224 DOI: 10.1038/Nature01160  0.751
2002 Zagrovic B, Snow CD, Shirts MR, Pande VS. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology. 323: 927-37. PMID 12417204 DOI: 10.1016/S0022-2836(02)00997-X  0.841
2002 Zagrovic B, Snow CD, Khaliq S, Shirts MR, Pande VS. Native-like mean structure in the unfolded ensemble of small proteins. Journal of Molecular Biology. 323: 153-64. PMID 12368107 DOI: 10.1016/S0022-2836(02)00888-4  0.83
2002 Sorin EJ, Engelhardt MA, Herschlag D, Pande VS. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. Journal of Molecular Biology. 317: 493-506. PMID 11955005 DOI: 10.1006/Jmbi.2002.5447  0.82
2002 Russell R, Millett IS, Tate MW, Kwok LW, Nakatani B, Gruner SM, Mochrie SG, Pande V, Doniach S, Herschlag D, Pollack L. Rapid compaction during RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 99: 4266-71. PMID 11929997 DOI: 10.1073/Pnas.072589599  0.336
2002 Zagrovic B, Snow CD, Shirts MR, Pande VS. Corrigendum to “Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwide-distributed Computing” Journal of Molecular Biology. 324: 1051. DOI: 10.1016/S0022-2836(02)01244-5  0.786
2001 Zagrovic B, Sorin EJ, Pande V. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. Journal of Molecular Biology. 313: 151-69. PMID 11601853 DOI: 10.1006/Jmbi.2001.5033  0.818
2001 Shirts MR, Pande VS. Mathematical analysis of coupled parallel simulations. Physical Review Letters. 86: 4983-7. PMID 11384401 DOI: 10.1103/Physrevlett.86.4983  0.653
2001 Elmer S, Pande VS. A New Twist on the Helix-Coil Transition:  A Non-Biological Helix with Protein-Like Intermediates and Traps The Journal of Physical Chemistry B. 105: 482-485. DOI: 10.1021/Jp0019761  0.481
2000 Shirts M, Pande VS. COMPUTING: Screen Savers of the World Unite! Science (New York, N.Y.). 290: 1903-4. PMID 17742054 DOI: 10.1126/Science.290.5498.1903  0.599
2000 Bryant Z, Pande VS, Rokhsar DS. Mechanical unfolding of a beta-hairpin using molecular dynamics. Biophysical Journal. 78: 584-9. PMID 10653773 DOI: 10.1016/S0006-3495(00)76618-5  0.42
2000 Pande VS, Grosberg AY, Tanaka T. Heteropolymer freezing and design: Towards physical models of protein folding Reviews of Modern Physics. 72: 259-314. DOI: 10.1103/Revmodphys.72.259  0.709
2000 Anderson RE, Pande VS, Radke CJ. Dynamic lattice Monte Carlo simulation of a model protein at an oil/water interface The Journal of Chemical Physics. 112: 9167-9185. DOI: 10.1063/1.481537  0.364
1999 Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proceedings of the National Academy of Sciences of the United States of America. 96: 9062-7. PMID 10430895 DOI: 10.1073/Pnas.96.16.9062  0.432
1999 Pande VS, Rokhsar DS. Folding pathway of a lattice model for proteins. Proceedings of the National Academy of Sciences of the United States of America. 96: 1273-8. PMID 9990014 DOI: 10.1073/Pnas.96.4.1273  0.416
1999 Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich E. On the role of conformational geometry in protein folding The Journal of Chemical Physics. 111: 10375-10380. DOI: 10.1063/1.480387  0.782
1998 Pande VS, Grosberg AYu, Tanaka T, Rokhsar DS. Pathways for protein folding: is a new view needed? Current Opinion in Structural Biology. 8: 68-79. PMID 9519298 DOI: 10.1016/S0959-440X(98)80012-2  0.606
1998 Pande VS, Rokhsar DS. Is the molten globule a third phase of proteins? Proceedings of the National Academy of Sciences of the United States of America. 95: 1490-4. PMID 9465042 DOI: 10.1073/Pnas.95.4.1490  0.432
1998 Chakraborty AK, Shakhnovich EI, Pande VS. Freezing of compact random heteropolymers with correlated sequence fluctuations The Journal of Chemical Physics. 108: 1683-1687. DOI: 10.1063/1.475539  0.51
1998 Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich ES. On the transition coordinate for protein folding The Journal of Chemical Physics. 108: 334-350. DOI: 10.1063/1.475393  0.708
1997 Pande VS, Grosberg AY, Tanaka T. Statistical mechanics of simple models of protein folding and design. Biophysical Journal. 73: 3192-210. PMID 9414231 DOI: 10.1016/S0006-3495(97)78345-0  0.622
1997 Pande VS, Grosberg AYu, Tanaka T. On the theory of folding kinetics for short proteins. Folding & Design. 2: 109-14. PMID 9135983 DOI: 10.1016/S1359-0278(97)00015-1  0.64
1997 Tanaka M, Grosberg AY, Pande VS, Tanaka T. Molecular dynamics study of the structure organization in a strongly coupled chain of charged particles Physical Review E. 56: 5798-5808. DOI: 10.1103/Physreve.56.5798  0.548
1997 Pande VS, Grosberg AY, Tanaka T. Thermodynamics of the coil to frozen globule transition in heteropolymers The Journal of Chemical Physics. 107: 5118-5124. DOI: 10.1063/1.474875  0.702
1997 Pande VS, Grosberg AY, Tanaka T. How to create polymers with protein-like capabilities: A theoretical suggestion Physica D: Nonlinear Phenomena. 107: 316-321. DOI: 10.1016/S0167-2789(97)00099-7  0.691
1996 Pande VS, Grosberg AY, Joerg C, Kardar M, Tanaka T. Freezing Transition of Compact Polyampholytes. Physical Review Letters. 77: 3565-3568. PMID 10062252 DOI: 10.1103/Physrevlett.77.3565  0.666
1996 Pande VS, Grosberg AY, Joerg C, Tanaka T. Is heteropolymer freezing well described by the random energy model? Physical Review Letters. 76: 3987-3990. PMID 10061163 DOI: 10.1103/Physrevlett.76.3987  0.68
1995 Pande VS, Grosberg AY, Tanaka T. Freezing transition of random heteropolymers consisting of an arbitrary set of monomers. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 51: 3381-3392. PMID 9963019 DOI: 10.1103/Physreve.51.3381  0.669
1995 Pande VS, Grosberg AY, Tanaka T. Phase diagram of an imprinted copolymer in a random external field Journal of Physics a: Mathematical and General. 28: 3657-3666. DOI: 10.1088/0305-4470/28/13/011  0.539
1995 Pande VS, Grosberg AY, Tanaka T. How accurate must potentials be for successful modeling of protein folding? The Journal of Chemical Physics. 103: 9482-9491. DOI: 10.1063/1.470009  0.699
1995 Tanaka T, Wang C, Pande V, Grosberg AY, English A, Masamune S, Gold H, Levy R, King K. Polymer gels that can recognize and recover molecules Faraday Discussions. 101: 201-206. DOI: 10.1039/Fd9950100201  0.495
1995 Pande VS, Grosberg AY, Tanaka T. Phase Diagram of Heteropolymers with an Imprinted Conformation Macromolecules. 28: 2218-2227. DOI: 10.1021/Ma00111A016  0.698
1994 Pande VS, Grosberg AY, Tanaka T. Thermodynamic procedure to synthesize heteropolymers that can renature to recognize a given target molecule Proceedings of the National Academy of Sciences of the United States of America. 91: 12976-12979. PMID 7809158 DOI: 10.1073/Pnas.91.26.12976  0.677
1994 Pande VS, Grosberg AY, Tanaka T. Nonrandomness in protein sequences: Evidence for a physically driven stage of evolution? Proceedings of the National Academy of Sciences of the United States of America. 91: 12972-12975. PMID 7809157 DOI: 10.1073/Pnas.91.26.12972  0.662
1994 Pande VS, Joerg C, Yu Grosberg A, Tanaka T. Enumerations of the Hamiltonian walks on a cubic sublattice Journal of Physics a: General Physics. 27: 6231-6236. DOI: 10.1088/0305-4470/27/18/030  0.518
1994 Pande VS, Grosberg AY, Tanaka T. Folding thermodynamics and kinetics of imprinted renaturable heteropolymers The Journal of Chemical Physics. 101: 8246-8257. DOI: 10.1063/1.468195  0.625
1994 Pande VS, Grosberg AY, Tanaka T. Phase diagram of imprinted copolymers Journal De Physique Ii. 4: 1771-1784. DOI: 10.1051/Jp2:1994231  0.7
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