 Connection
Michael Shirts to Protein Binding
This is a "connection" page, showing publications Michael Shirts has written about Protein Binding.
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Connection Strength |
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0.616 |
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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: 0.130
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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: 0.092
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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: 0.076
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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: 0.069
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Shirts MR. Best practices in free energy calculations for drug design. Methods Mol Biol. 2012; 819:425-67.
Score: 0.066
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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: 0.049
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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: 0.029
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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: 0.023
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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: 0.017
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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: 0.016
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Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol. 2011 Apr; 21(2):150-60.
Score: 0.016
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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: 0.011
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Sorin EJ, Rhee YM, Shirts MR, Pande VS. The solvation interface is a determining factor in peptide conformational preferences. J Mol Biol. 2006 Feb 10; 356(1):248-56.
Score: 0.011
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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: 0.011
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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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