Michael R. Shirts, Ph.D. - Publications

Affiliations: 
2005 Stanford University, Palo Alto, CA 
Area:
theoretical methods to understand the physical properties of biological molecules

55 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
2020 Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5  0.88
2018 Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward learned chemical perception of force field typing rules. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/Acs.Jctc.8B00821  0.88
2018 Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Eastman PK. Escaping atom types in force fields using direct chemical perception. Journal of Chemical Theory and Computation. PMID 30351006 DOI: 10.1021/Acs.Jctc.8B00640  0.88
2017 Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. Journal of Chemical and Engineering Data. 62: 1559-1569. PMID 29056756 DOI: 10.1021/Acs.Jced.7B00104  0.88
2017 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Erratum to: Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 28752343 DOI: 10.1007/S10822-017-0043-4  0.6
2016 Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design. PMID 27787702 DOI: 10.1007/S10822-016-9977-1  0.6
2016 Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. 30: 927-944. PMID 27677750 DOI: 10.1007/S10822-016-9954-8  0.6
2016 Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Overview of the SAMPL5 host-guest challenge: Are we doing better? Journal of Computer-Aided Molecular Design. PMID 27658802 DOI: 10.1007/S10822-016-9974-4  0.6
2015 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. Journal of Chemical Theory and Computation. 11: 1347. PMID 26579779 DOI: 10.1021/Acs.Jctc.5B00154  0.6
2015 Slovin MR, Shirts MR. Identifying Differences and Similarities in Static and Dynamic Contact Angles between Nanoscale and Microscale Textured Surfaces Using Molecular Dynamics Simulations. Langmuir : the Acs Journal of Surfaces and Colloids. 31: 7980-90. PMID 26110823 DOI: 10.1021/Acs.Langmuir.5B00842  0.88
2015 Klimovich PV, Shirts MR, Mobley DL. Guidelines for the analysis of free energy calculations. Journal of Computer-Aided Molecular Design. 29: 397-411. PMID 25808134 DOI: 10.1007/S10822-015-9840-9  0.6
2015 Basconi JE, Carta G, Shirts MR. Effects of polymer graft properties on protein adsorption and transport in ion exchange chromatography: a multiscale modeling study. Langmuir : the Acs Journal of Surfaces and Colloids. 31: 4176-87. PMID 25785668 DOI: 10.1021/La504768G  0.88
2014 Naden LN, Pham TT, Shirts MR. Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites. Journal of Chemical Theory and Computation. 10: 1128-49. PMID 26580188 DOI: 10.1021/Ct4009188  0.88
2014 Basconi JE, Carta G, Shirts MR. Multiscale modeling of protein adsorption and transport in macroporous and polymer-grafted ion exchangers Aiche Journal. 60: 3888-3901. DOI: 10.1002/Aic.14621  0.88
2013 Shirts MR. Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles. Journal of Chemical Theory and Computation. 9: 909-26. PMID 26588735 DOI: 10.1021/Ct300688P  0.01
2013 Wang K, Chodera JD, Yang Y, Shirts MR. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. Journal of Computer-Aided Molecular Design. 27: 989-1007. PMID 24297454 DOI: 10.1007/S10822-013-9689-8  0.88
2013 Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy. Journal of the American Chemical Society. 135: 18831-9. PMID 24279927 DOI: 10.1021/Ja407287F  0.88
2013 Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics (Oxford, England). 29: 845-54. PMID 23407358 DOI: 10.1093/Bioinformatics/Btt055  0.88
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, 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  0.88
2013 Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods in Molecular Biology (Clifton, N.J.). 924: 271-311. PMID 23034753 DOI: 10.1007/978-1-62703-017-5_11  0.6
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, 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  0.88
2013 Basconi J, Carta G, Shirts MR. Elucidating the details of protein transport in polymer-grafted ion exchangers through multi-scale modeling Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 1034.  0.88
2013 Wang K, Yang Y, Chodera JD, Shirts MR. Identifying ligand binding sites and poses using Hamiltonian replica exchange molecular dynamics: Model systems and a validation study using the astex diverse set Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 622.  0.88
2012 Fuller JC, Jackson RM, Shirts MR. Configurational preferences of arylamide α-helix mimetics via alchemical free energy calculations of relative binding affinities. The Journal of Physical Chemistry. B. 116: 10856-69. PMID 22920218 DOI: 10.1021/Jp209041X  0.88
2012 Fuller JC, Jackson RM, Edwards TA, Wilson AJ, Shirts MR. Modeling of arylamide helix mimetics in the p53 peptide binding site of hDM2 suggests parallel and anti-parallel conformations are both stable. Plos One. 7: e43253. PMID 22916232 DOI: 10.1371/Journal.Pone.0043253  0.88
2012 Bu L, Nimlos MR, Shirts MR, Ståhlberg J, Himmel ME, Crowley MF, Beckham GT. Product binding varies dramatically between processive and nonprocessive cellulase enzymes. The Journal of Biological Chemistry. 287: 24807-13. PMID 22648408 DOI: 10.1074/Jbc.M112.365510  0.88
2012 Pham TT, Shirts MR. Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase. The Journal of Chemical Physics. 136: 124120. PMID 22462848 DOI: 10.1063/1.3697833  0.88
2012 Zhang A, Singh SK, Shirts MR, Kumar S, Fernandez EJ. Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange. Pharmaceutical Research. 29: 236-50. PMID 21805212 DOI: 10.1007/S11095-011-0538-Y  0.88
2011 Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. The Journal of Chemical Physics. 135: 194110. PMID 22112069 DOI: 10.1063/1.3660669  0.88
2011 Pham TT, Shirts MR. Identifying low variance pathways for free energy calculations of molecular transformations in solution phase. The Journal of Chemical Physics. 135: 034114. PMID 21786994 DOI: 10.1063/1.3607597  0.88
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  0.88
2011 Bu L, Beckham GT, Shirts MR, Nimlos MR, Adney WS, Himmel ME, Crowley MF. Probing carbohydrate product expulsion from a processive cellulase with multiple absolute binding free energy methods. The Journal of Biological Chemistry. 286: 18161-9. PMID 21454590 DOI: 10.1074/Jbc.M110.212076  0.88
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  0.88
2009 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. Journal of Chemical Theory and Computation. 5: 350-358. PMID 20150953 DOI: 10.1021/Ct800409D  0.88
2008 Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics. 129: 124105. PMID 19045004 DOI: 10.1063/1.2978177  0.88
2008 Shirts MR, Chodera JD. Statistically optimal free energy estimates from sparsely chosen states Aiche Annual Meeting, Conference Proceedings 0.88
2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 3: 640-8. PMID 26637042 DOI: 10.1021/Ct600129F  0.6
2007 Zhu K, Shirts MR, Friesner RA. Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program:  Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects. Journal of Chemical Theory and Computation. 3: 2108-19. PMID 26636204 DOI: 10.1021/Ct700166F  0.6
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  0.88
2007 Zhu K, Shirts MR, Friesner RA. Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects Journal of Chemical Theory and Computation. 3: 2108-2119. DOI: 10.1021/ct700166f  0.88
2007 Zhu K, Shirts MR, Friesner RA, Jacobson MP. Multiscale optimization of a truncated newton minimization algorithm and application to proteins and protein-ligand complexes Journal of Chemical Theory and Computation. 3: 640-648. DOI: 10.1021/ct600129f  0.88
2007 Shirts MR, Mobley DL, Chodera JD. Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? Annual Reports in Computational Chemistry. 3: 41-59. DOI: 10.1016/S1574-1400(07)03004-6  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
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  0.88
2002 Shirts RB, Shirts MR. Deviations from the Boltzmann distribution in small microcanonical quantum systems: Two approximate one-particle energy distributions Journal of Chemical Physics. 117: 5564-5575. DOI: 10.1063/1.1503306  0.88
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  0.88
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  1
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