 Connection
Michael Shirts to Ligands
This is a "connection" page, showing publications Michael Shirts has written about Ligands.
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Connection Strength |
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0.805 |
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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: 0.425
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Shirts MR. Best practices in free energy calculations for drug design. Methods Mol Biol. 2012; 819:425-67.
Score: 0.076
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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: 0.057
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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Woojuh J, Xing Z, Cutler SR, Kaar JL, Shirts MR, Whitehead TA. Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS Chem Biol. 2024 08 16; 19(8):1757-1772.
Score: 0.045
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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: 0.042
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Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, Gilson MK, Chodera JD, Bayly CI, Mobley DL, Wang LP. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. J Chem Theory Comput. 2021 Oct 12; 17(10):6262-6280.
Score: 0.037
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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: 0.037
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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: 0.033
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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: 0.026
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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: 0.013
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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: 0.012
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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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