Kim B - Search Results

1

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: kim b. 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

2

Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor.

Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Goldfeld DA, et al. Among authors: kim b. J Phys Chem B. 2015 Jan 22;119(3):824-35. doi: 10.1021/jp5053612. Epub 2014 Nov 26. J Phys Chem B. 2015. PMID: 25395044

3

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery.

Wang L, Deng Y, Wu Y, Kim B, LeBard DN, Wandschneider D, Beachy M, Friesner RA, Abel R. Wang L, et al. Among authors: kim b. J Chem Theory Comput. 2017 Jan 10;13(1):42-54. doi: 10.1021/acs.jctc.6b00991. Epub 2016 Dec 9. J Chem Theory Comput. 2017. PMID: 27933808

4

Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

Young T, Abel R, Kim B, Berne BJ, Friesner RA. Young T, et al. Among authors: kim b. Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):808-13. doi: 10.1073/pnas.0610202104. Epub 2007 Jan 4. Proc Natl Acad Sci U S A. 2007. PMID: 17204562 Free PMC article.

5

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization.

Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, Sherman W. Beuming T, et al. Among authors: kim b. Proteins. 2012 Mar;80(3):871-83. doi: 10.1002/prot.23244. Epub 2011 Dec 16. Proteins. 2012. PMID: 22223256

6

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.

Wang L, Deng Y, Knight JL, Wu Y, Kim B, Sherman W, Shelley JC, Lin T, Abel R. Wang L, et al. Among authors: kim b. J Chem Theory Comput. 2013 Feb 12;9(2):1282-93. doi: 10.1021/ct300911a. Epub 2013 Jan 30. J Chem Theory Comput. 2013. PMID: 26588769

7

Serial replica exchange.

Hagen M, Kim B, Liu P, Friesner RA, Berne BJ. Hagen M, et al. Among authors: kim b. 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.

8

Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid Water.

Harder E, Kim B, Friesner RA, Berne BJ. Harder E, et al. Among authors: kim b. J Chem Theory Comput. 2005 Jan;1(1):169-80. doi: 10.1021/ct049914s. J Chem Theory Comput. 2005. PMID: 26641127

9

A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor.

Lyman E, Higgs C, Kim B, Lupyan D, Shelley JC, Farid R, Voth GA. Lyman E, et al. Among authors: kim b. Structure. 2009 Dec 9;17(12):1660-1668. doi: 10.1016/j.str.2009.10.010. Structure. 2009. PMID: 20004169 Free PMC article.

10

Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

Liu P, Kim B, Friesner RA, Berne BJ. Liu P, et al. Among authors: kim b. Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13749-54. doi: 10.1073/pnas.0506346102. Epub 2005 Sep 19. Proc Natl Acad Sci U S A. 2005. PMID: 16172406 Free PMC article.

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