Michael R. Shirts
Michael R. Shirts
Associate 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
49782013
Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
11082008
Screen savers of the world unite!
M Shirts, VS Pande
Science 290 (5498), 1903-1904, 2000
6452000
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
6422003
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
4862012
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
4632003
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
4392005
Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods
MR Shirts, E Bair, G Hooker, VS Pande
Physical review letters 91 (14), 140601, 2003
4292003
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
4172011
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
3772009
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
3562002
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
3412005
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
3242009
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
2642015
Alchemical free energy calculations: Ready for prime time?
MR Shirts, DL Mobley, JD Chodera
Annual Reports in Computational Chemistry 3, 41-59, 2007
2102007
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
2102005
Native-like mean structure in the unfolded ensemble of small proteins
B Zagrovic, CD Snow, S Khaliq, MR Shirts, VS Pande
Journal of molecular biology 323 (1), 153-164, 2002
2042002
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
2012013
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
1762007
Mathematical analysis of coupled parallel simulations
MR Shirts, VS Pande
Physical review letters 86 (22), 4983-4987, 2001
1322001
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