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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: lupyan d. 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: lupyan d. 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
An analysis of core deformations in protein superfamilies.
Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. Leo-Macias A, et al. Among authors: lupyan d. Biophys J. 2005 Feb;88(2):1291-9. doi: 10.1529/biophysj.104.052449. Epub 2004 Nov 12. Biophys J. 2005. PMID: 15542556 Free PMC article.
Core deformations in protein families: a physical perspective.
Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. Leo-Macias A, et al. Among authors: lupyan d. Biophys Chem. 2005 Apr 1;115(2-3):125-8. doi: 10.1016/j.bpc.2004.12.016. Epub 2005 Jan 18. Biophys Chem. 2005. PMID: 15752593
14 results