 Connection
Michael Shirts to Thermodynamics
This is a "connection" page, showing publications Michael Shirts has written about Thermodynamics.
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Connection Strength |
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3.912 |
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Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput. 2022 Jun 14; 18(6):3577-3592.
Score: 0.659
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Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. J Chem Theory Comput. 2022 Jun 14; 18(6):3566-3576.
Score: 0.659
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Paliwal H, Shirts MR. Multistate reweighting and configuration mapping together accelerate the efficiency of thermodynamic calculations as a function of molecular geometry by orders of magnitude. J Chem Phys. 2013 Apr 21; 138(15):154108.
Score: 0.352
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Shirts MR, Mobley DL. An introduction to best practices in free energy calculations. Methods Mol Biol. 2013; 924:271-311.
Score: 0.345
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Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. J Chem Phys. 2011 Nov 21; 135(19):194110.
Score: 0.319
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Shirts MR, Pande VS. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. J Chem Phys. 2005 Apr 01; 122(13):134508.
Score: 0.202
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Shirts MR, Ferguson AL. Statistically Optimal Continuous Free Energy Surfaces from Biased Simulations and Multistate Reweighting. J Chem Theory Comput. 2020 Jul 14; 16(7):4107-4125.
Score: 0.145
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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, Mobley DL, Chodera JD. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J Comput Aided Mol Des. 2020 05; 34(5):601-633.
Score: 0.141
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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. J Comput Aided Mol Des. 2017 01; 31(1):147-161.
Score: 0.112
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Dybeck EC, K?nig G, Brooks BR, Shirts MR. Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials. J Chem Theory Comput. 2016 Apr 12; 12(4):1466-80.
Score: 0.108
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Zhong ED, Shirts MR. Thermodynamics of coupled protein adsorption and stability using hybrid Monte Carlo simulations. Langmuir. 2014 May 06; 30(17):4952-61.
Score: 0.094
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Monroe JI, Shirts MR. Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. J Comput Aided Mol Des. 2014 Apr; 28(4):401-15.
Score: 0.094
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Wang K, Chodera JD, Yang Y, Shirts MR. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des. 2013 Dec; 27(12):989-1007.
Score: 0.092
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Fuller JC, Jackson RM, Shirts MR. Configurational preferences of arylamide a-helix mimetics via alchemical free energy calculations of relative binding affinities. J Phys Chem B. 2012 Sep 06; 116(35):10856-69.
Score: 0.084
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Shirts MR. Best practices in free energy calculations for drug design. Methods Mol Biol. 2012; 819:425-67.
Score: 0.080
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Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys. 2008 Sep 28; 129(12):124105.
Score: 0.064
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Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. J Phys Chem B. 2007 Nov 15; 111(45):13052-63.
Score: 0.060
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Shirts MR, Pande VS. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. J Chem Phys. 2005 Apr 08; 122(14):144107.
Score: 0.050
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Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, Chodera JD, Bayly CI, Shirts MR, Mobley DL. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. J Chem Theory Comput. 2023 Jun 13; 19(11):3251-3275.
Score: 0.044
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Zhang S, Hahn DF, Shirts MR, Voelz VA. Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies. J Chem Theory Comput. 2021 Oct 12; 17(10):6536-6547.
Score: 0.039
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Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL. Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge. J Comput Aided Mol Des. 2016 11; 30(11):927-944.
Score: 0.028
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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? J Comput Aided Mol Des. 2017 01; 31(1):1-19.
Score: 0.028
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Payne CM, Jiang W, Shirts MR, Himmel ME, Crowley MF, Beckham GT. Glycoside hydrolase processivity is directly related to oligosaccharide binding free energy. J Am Chem Soc. 2013 Dec 18; 135(50):18831-9.
Score: 0.023
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Bu L, Nimlos MR, Shirts MR, St?hlberg J, Himmel ME, Crowley MF, Beckham GT. Product binding varies dramatically between processive and nonprocessive cellulase enzymes. J Biol Chem. 2012 Jul 13; 287(29):24807-13.
Score: 0.021
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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. J Biol Chem. 2011 May 20; 286(20):18161-9.
Score: 0.019
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Jayachandran G, Shirts MR, Park S, Pande VS. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys. 2006 Aug 28; 125(8):084901.
Score: 0.014
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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. J Chem Phys. 2005 Aug 22; 123(8):084108.
Score: 0.013
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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. 2003 Jan; 68(1):91-109.
Score: 0.011
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Zagrovic B, Snow CD, Shirts MR, Pande VS. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J Mol Biol. 2002 Nov 08; 323(5):927-37.
Score: 0.011
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Connection Strength
The connection strength for concepts is the sum of the scores for each matching publication.
Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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