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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: berne bj. 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
Serial replica exchange.
Hagen M, Kim B, Liu P, Friesner RA, Berne BJ. Hagen M, et al. Among authors: berne bj. J Phys Chem B. 2007 Feb 15;111(6):1416-23. doi: 10.1021/jp064479e. Epub 2007 Jan 24. J Phys Chem B. 2007. PMID: 17249714 Free PMC article.
Ligand binding to protein-binding pockets with wet and dry regions.
Wang L, Berne BJ, Friesner RA. Wang L, et al. Among authors: berne bj. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1326-30. doi: 10.1073/pnas.1016793108. Epub 2011 Jan 4. Proc Natl Acad Sci U S A. 2011. PMID: 21205906 Free PMC article.
In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young T, Farid R, Berne BJ, Friesner RA (2008) J Am Chem Soc 130:2817-2831] of the popular MM-GBSA approach to binding affinity cal …
In addition, WaterMap when combined with the cavity contribution is more predictive than at least one specific implementation [Abel R, Young …
Integrated Modeling Program, Applied Chemical Theory (IMPACT).
Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM. Banks JL, et al. Among authors: berne bj. J Comput Chem. 2005 Dec;26(16):1752-80. doi: 10.1002/jcc.20292. J Comput Chem. 2005. PMID: 16211539 Free PMC article. Review.
101 results