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Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.
Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. Wang L, et al. Among authors: knight jl. J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12. J Am Chem Soc. 2015. PMID: 25625324
OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. Harder E, et al. Among authors: knight jl. J Chem Theory Comput. 2016 Jan 12;12(1):281-96. doi: 10.1021/acs.jctc.5b00864. Epub 2015 Dec 1. J Chem Theory Comput. 2016. PMID: 26584231
Deconstructing activation events in rhodopsin.
Laricheva EN, Arora K, Knight JL, Brooks CL 3rd. Laricheva EN, et al. Among authors: knight jl. J Am Chem Soc. 2013 Jul 31;135(30):10906-9. doi: 10.1021/ja4042687. Epub 2013 Jul 22. J Am Chem Soc. 2013. PMID: 23841875 Free PMC article.
Lambda-dynamics free energy simulation methods.
Knight JL, Brooks CL 3rd. Knight JL, et al. J Comput Chem. 2009 Aug;30(11):1692-700. doi: 10.1002/jcc.21295. J Comput Chem. 2009. PMID: 19421993 Free PMC article. Review.
pH-dependent dynamics of complex RNA macromolecules.
Goh GB, Knight JL, Brooks CL 3rd. Goh GB, et al. Among authors: knight jl. J Chem Theory Comput. 2013 Feb 12;9(2):935-943. doi: 10.1021/ct300942z. Epub 2013 Jan 3. J Chem Theory Comput. 2013. PMID: 23525495 Free PMC article.
95 results