Beuming T - 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: beuming t. 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

High-energy water sites determine peptide binding affinity and specificity of PDZ domains.

Beuming T, Farid R, Sherman W. Beuming T, et al. Protein Sci. 2009 Aug;18(8):1609-19. doi: 10.1002/pro.177. Protein Sci. 2009. PMID: 19569188 Free PMC article.

3

Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors.

Goldfeld DA, Zhu K, Beuming T, Friesner RA. Goldfeld DA, et al. Among authors: beuming t. Proc Natl Acad Sci U S A. 2011 May 17;108(20):8275-80. doi: 10.1073/pnas.1016951108. Epub 2011 May 2. Proc Natl Acad Sci U S A. 2011. PMID: 21536915 Free PMC article.

4

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. Proteins. 2012 Mar;80(3):871-83. doi: 10.1002/prot.23244. Epub 2011 Dec 16. Proteins. 2012. PMID: 22223256

5

Loop prediction for a GPCR homology model: algorithms and results.

Goldfeld DA, Zhu K, Beuming T, Friesner RA. Goldfeld DA, et al. Among authors: beuming t. Proteins. 2013 Feb;81(2):214-28. doi: 10.1002/prot.24178. Epub 2012 Sep 29. Proteins. 2013. PMID: 22965891

6

Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines.

Beuming T, Sherman W. Beuming T, et al. J Chem Inf Model. 2012 Dec 21;52(12):3263-77. doi: 10.1021/ci300411b. Epub 2012 Nov 15. J Chem Inf Model. 2012. PMID: 23121495

7

Structure-based virtual screening of MT2 melatonin receptor: influence of template choice and structural refinement.

Pala D, Beuming T, Sherman W, Lodola A, Rivara S, Mor M. Pala D, et al. Among authors: beuming t. J Chem Inf Model. 2013 Apr 22;53(4):821-35. doi: 10.1021/ci4000147. Epub 2013 Apr 9. J Chem Inf Model. 2013. PMID: 23541165

8

Improved docking of polypeptides with Glide.

Tubert-Brohman I, Sherman W, Repasky M, Beuming T. Tubert-Brohman I, et al. Among authors: beuming t. J Chem Inf Model. 2013 Jul 22;53(7):1689-99. doi: 10.1021/ci400128m. Epub 2013 Jul 10. J Chem Inf Model. 2013. PMID: 23800267

9

Predicting GPCR promiscuity using binding site features.

Levit A, Beuming T, Krilov G, Sherman W, Niv MY. Levit A, et al. Among authors: beuming t. J Chem Inf Model. 2014 Jan 27;54(1):184-94. doi: 10.1021/ci400552z. Epub 2013 Dec 27. J Chem Inf Model. 2014. PMID: 24328091

10

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor.

Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP. Lenselink EB, et al. Among authors: beuming t. J Chem Inf Model. 2014 Jun 23;54(6):1737-46. doi: 10.1021/ci5000455. Epub 2014 Jun 3. J Chem Inf Model. 2014. PMID: 24835542

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