| GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit S Pronk, S Páll, R Schulz, P Larsson, P Bjelkmar, R Apostolov, MR Shirts, ... Bioinformatics, 2013 | 7512 | 2013 |
| Statistically optimal analysis of samples from multiple equilibrium states MR Shirts, JD Chodera The Journal of chemical physics 129, 124105, 2008 | 1869 | 2008 |
| Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins MR Shirts, JW Pitera, WC Swope, VS Pande The Journal of chemical physics 119 (11), 5740-5761, 2003 | 768 | 2003 |
| Screen savers of the world unite! M Shirts, VS Pande Science 290 (5498), 1903-1904, 2000 | 729 | 2000 |
| OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation P Eastman, MS Friedrichs, JD Chodera, RJ Radmer, CM Bruns, JP Ku, ... Journal of chemical theory and computation 9 (1), 461-469, 2012 | 712 | 2012 |
| Alchemical free energy methods for drug discovery: progress and challenges JD Chodera, DL Mobley, MR Shirts, RW Dixon, K Branson, VS Pande Current opinion in structural biology 21 (2), 150-160, 2011 | 622 | 2011 |
| Equilibrium Free Energies from Nonequilibrium Measurements<? format?> Using Maximum-Likelihood Methods MR Shirts, E Bair, G Hooker, VS Pande Physical review letters 91 (14), 140601, 2003 | 560 | 2003 |
| Guidelines for the analysis of free energy calculations PV Klimovich, MR Shirts, DL Mobley Journal of computer-aided molecular design 29 (5), 397-411, 2015 | 505 | 2015 |
| Solvation free energies of amino acid side chain analogs for common molecular mechanics water models MR Shirts, VS Pande The Journal of chemical physics 122, 134508, 2005 | 495 | 2005 |
| Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing VS Pande, I Baker, J Chapman, SP Elmer, S Khaliq, SM Larson, YM Rhee, ... Biopolymers: Original Research on Biomolecules 68 (1), 91-109, 2003 | 484 | 2003 |
| Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration MR Shirts, VS Pande The Journal of chemical physics 122 (14), 144107-144107-16, 2005 | 441 | 2005 |
| Folding@ Home and Genome@ Home: Using distributed computing to tackle previously intractable problems in computational biology SM Larson, CD Snow, M Shirts, VS Pande arXiv preprint arXiv:0901.0866, 2009 | 433 | 2009 |
| Effects of temperature control algorithms on transport properties and kinetics in molecular dynamics simulations JE Basconi, MR Shirts Journal of chemical theory and computation 9 (7), 2887-2899, 2013 | 407 | 2013 |
| Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing B Zagrovic, CD Snow, MR Shirts, VS Pande Journal of molecular biology 323 (5), 927-937, 2002 | 392 | 2002 |
| Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations DL Mobley, CI Bayly, MD Cooper, MR Shirts, KA Dill Journal of chemical theory and computation 5 (2), 350-358, 2009 | 390 | 2009 |
| Alchemical free energy calculations: Ready for prime time? MR Shirts, DL Mobley, JD Chodera Annual Reports in Computational Chemistry 3, 41-59, 2007 | 264 | 2007 |
| Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset MR Shirts, C Klein, JM Swails, J Yin, MK Gilson, DL Mobley, DA Case, ... Journal of Computer-Aided Molecular Design 31 (1), 147-161, 2017 | 260 | 2017 |
| Accurate and efficient corrections for missing dispersion interactions in molecular simulations MR Shirts, DL Mobley, JD Chodera, VS Pande The journal of physical chemistry B 111 (45), 13052-13063, 2007 | 236 | 2007 |
| Direct calculation of the binding free energies of FKBP ligands H Fujitani, Y Tanida, M Ito, G Jayachandran, CD Snow, MR Shirts, ... The Journal of chemical physics 123, 084108, 2005 | 236 | 2005 |
| Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database G Duarte Ramos Matos, DY Kyu, HH Loeffler, JD Chodera, MR Shirts, ... Journal of Chemical & Engineering Data 62 (5), 1559-1569, 2017 | 227 | 2017 |
David MobleyProfessor, University of California, Irvine確認したメール アドレス: uci.edu
