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Michael R. Shirts
Michael R. Shirts
Other namesMichael Shirts
Professor of Chemical and Biological Engineering, University of Colorado Boulder
Verified email at colorado.edu - Homepage
Title
Cited by
Cited by
Year
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
73802013
Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
18312008
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
7612003
Screen savers of the world unite!
M Shirts, VS Pande
Science 290 (5498), 1903-1904, 2000
7242000
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
7022012
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
6062011
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
5542003
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
4912005
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
4872015
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
4832003
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
4342005
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
4302009
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
3952013
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
3902002
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
3892009
Alchemical free energy calculations: Ready for prime time?
MR Shirts, DL Mobley, JD Chodera
Annual Reports in Computational Chemistry 3, 41-59, 2007
2632007
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
2482017
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
2362005
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
2322007
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
2212017
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