Lupyan D - 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: 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

2

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

3

Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics.

Yu HS, Gao C, Lupyan D, Wu Y, Kimura T, Wu C, Jacobson L, Harder E, Abel R, Wang L. Yu HS, et al. Among authors: lupyan d. J Chem Inf Model. 2019 Sep 23;59(9):3955-3967. doi: 10.1021/acs.jcim.9b00268. Epub 2019 Sep 12. J Chem Inf Model. 2019. PMID: 31425654

4

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: lupyan d. Structure. 2009 Dec 9;17(12):1660-1668. doi: 10.1016/j.str.2009.10.010. Structure. 2009. PMID: 20004169 Free PMC article.

5

Improving the Accuracy of Protein Thermostability Predictions for Single Point Mutations.

Duan J, Lupyan D, Wang L. Duan J, et al. Among authors: lupyan d. Biophys J. 2020 Jul 7;119(1):115-127. doi: 10.1016/j.bpj.2020.05.020. Epub 2020 May 29. Biophys J. 2020. PMID: 32533939 Free PMC article.

6

Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

Lupyan D, Abramov YA, Sherman W. Lupyan D, et al. J Comput Aided Mol Des. 2012 Nov;26(11):1195-205. doi: 10.1007/s10822-012-9610-x. Epub 2012 Oct 6. J Comput Aided Mol Des. 2012. PMID: 23053737

7

Effective mast cell degranulating peptide inhibitors of the IgE/Fc epsilonRI receptor interaction.

Buku A, Keselman I, Lupyan D, Mezei M, Price JA. Buku A, et al. Among authors: lupyan d. Chem Biol Drug Des. 2008 Aug;72(2):133-9. doi: 10.1111/j.1747-0285.2008.00684.x. Epub 2008 Jul 10. Chem Biol Drug Des. 2008. PMID: 18624811

8

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.

9

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

10

A molecular dynamics investigation of lipid bilayer perturbation by PIP2.

Lupyan D, Mezei M, Logothetis DE, Osman R. Lupyan D, et al. Biophys J. 2010 Jan 20;98(2):240-7. doi: 10.1016/j.bpj.2009.09.063. Biophys J. 2010. PMID: 20338845 Free PMC article.

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