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Items: 43

1.

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.

Ghanakota P, van Vlijmen H, Sherman W, Beuming T.

J Chem Inf Model. 2018 Apr 23;58(4):784-793. doi: 10.1021/acs.jcim.7b00487. Epub 2018 Apr 11.

PMID:
29617116
2.

Identification of a Mycothiol-Dependent Nitroreductase from Mycobacterium tuberculosis.

Negri A, Javidnia P, Mu R, Zhang X, Vendome J, Gold B, Roberts J, Barman D, Ioerger T, Sacchettini JC, Jiang X, Burns-Huang K, Warrier T, Ling Y, Warren JD, Oren DA, Beuming T, Wang H, Wu J, Li H, Rhee KY, Nathan CF, Liu G, Somersan-Karakaya S.

ACS Infect Dis. 2018 May 11;4(5):771-787. doi: 10.1021/acsinfecdis.7b00111. Epub 2018 Feb 21.

3.

Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma.

Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM.

Sci Rep. 2018 Jan 15;8(1):720. doi: 10.1038/s41598-017-18956-w.

4.

Editorial: Computer Aided Structure-based Lead Optimization.

Beuming T, Shi L.

Curr Top Med Chem. 2017;17(23):2575-2576. doi: 10.2174/156802661723170808161306. No abstract available.

PMID:
28889794
5.

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

Cappel D, Sherman W, Beuming T.

Curr Top Med Chem. 2017;17(23):2586-2598. doi: 10.2174/1568026617666170414141452. Review.

PMID:
28413953
6.

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite.

Bhachoo J, Beuming T.

Methods Mol Biol. 2017;1561:235-254. doi: 10.1007/978-1-4939-6798-8_14.

PMID:
28236242
7.

Relative Binding Free Energy Calculations Applied to Protein Homology Models.

Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W.

J Chem Inf Model. 2016 Dec 27;56(12):2388-2400. doi: 10.1021/acs.jcim.6b00362. Epub 2016 Nov 18.

8.

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor.

Lenselink EB, Beuming T, van Veen C, Massink A, Sherman W, van Vlijmen HW, IJzerman AP.

J Comput Aided Mol Des. 2016 Oct;30(10):863-874. Epub 2016 Sep 15.

9.

Molecular dynamics techniques for modeling G protein-coupled receptors.

McRobb FM, Negri A, Beuming T, Sherman W.

Curr Opin Pharmacol. 2016 Oct;30:69-75. doi: 10.1016/j.coph.2016.07.001. Epub 2016 Aug 3. Review.

PMID:
27490828
10.

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation.

Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J, Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, Beuming T.

ACS Omega. 2016 Aug 31;1(2):293-304. doi: 10.1021/acsomega.6b00086. Epub 2016 Aug 30.

11.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins.

Kamps JJ, Huang J, Poater J, Xu C, Pieters BJ, Dong A, Min J, Sherman W, Beuming T, Matthias Bickelhaupt F, Li H, Mecinović J.

Nat Commun. 2015 Nov 18;6:8911. doi: 10.1038/ncomms9911.

12.

Docking and Virtual Screening Strategies for GPCR Drug Discovery.

Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W.

Methods Mol Biol. 2015;1335:251-76. doi: 10.1007/978-1-4939-2914-6_17.

PMID:
26260606
13.

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.

J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12.

PMID:
25625324
14.

What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?

Michino M, Beuming T, Donthamsetti P, Newman AH, Javitch JA, Shi L.

Pharmacol Rev. 2015;67(1):198-213. doi: 10.1124/pr.114.009944. Review.

15.

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.

J Phys Chem B. 2015 Jan 22;119(3):824-35. doi: 10.1021/jp5053612. Epub 2014 Nov 26.

PMID:
25395044
16.

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.

J Chem Inf Model. 2014 Jun 23;54(6):1737-46. doi: 10.1021/ci5000455. Epub 2014 Jun 3.

PMID:
24835542
17.

Discovery and characterization of a G protein-biased agonist that inhibits β-arrestin recruitment to the D2 dopamine receptor.

Free RB, Chun LS, Moritz AE, Miller BN, Doyle TB, Conroy JL, Padron A, Meade JA, Xiao J, Hu X, Dulcey AE, Han Y, Duan L, Titus S, Bryant-Genevier M, Barnaeva E, Ferrer M, Javitch JA, Beuming T, Shi L, Southall NT, Marugan JJ, Sibley DR.

Mol Pharmacol. 2014 Jul;86(1):96-105. doi: 10.1124/mol.113.090563. Epub 2014 Apr 22.

18.

Conformational changes in dopamine transporter intracellular regions upon cocaine binding and dopamine translocation.

Dehnes Y, Shan J, Beuming T, Shi L, Weinstein H, Javitch JA.

Neurochem Int. 2014 Jul;73:4-15. doi: 10.1016/j.neuint.2014.02.003. Epub 2014 Feb 24.

19.

Predicting GPCR promiscuity using binding site features.

Levit A, Beuming T, Krilov G, Sherman W, Niv MY.

J Chem Inf Model. 2014 Jan 27;54(1):184-94. doi: 10.1021/ci400552z. Epub 2013 Dec 27.

PMID:
24328091
20.

A single glycine in extracellular loop 1 is the critical determinant for pharmacological specificity of dopamine D2 and D3 receptors.

Michino M, Donthamsetti P, Beuming T, Banala A, Duan L, Roux T, Han Y, Trinquet E, Newman AH, Javitch JA, Shi L.

Mol Pharmacol. 2013 Dec;84(6):854-64. doi: 10.1124/mol.113.087833. Epub 2013 Sep 23.

21.

Improved docking of polypeptides with Glide.

Tubert-Brohman I, Sherman W, Repasky M, Beuming T.

J Chem Inf Model. 2013 Jul 22;53(7):1689-99. doi: 10.1021/ci400128m. Epub 2013 Jul 10.

PMID:
23800267
22.

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

Li J, Jonsson AL, Beuming T, Shelley JC, Voth GA.

J Am Chem Soc. 2013 Jun 12;135(23):8749-59. doi: 10.1021/ja404391q. Epub 2013 May 29.

23.

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.

J Chem Inf Model. 2013 Apr 22;53(4):821-35. doi: 10.1021/ci4000147. Epub 2013 Apr 9.

PMID:
23541165
24.

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

Beuming T, Sherman W.

J Chem Inf Model. 2012 Dec 21;52(12):3263-77. doi: 10.1021/ci300411b. Epub 2012 Nov 15.

PMID:
23121495
25.

Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter.

Plenge P, Shi L, Beuming T, Te J, Newman AH, Weinstein H, Gether U, Loland CJ.

J Biol Chem. 2012 Nov 16;287(47):39316-26. doi: 10.1074/jbc.M112.371765. Epub 2012 Sep 24.

26.

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

Goldfeld DA, Zhu K, Beuming T, Friesner RA.

Proteins. 2013 Feb;81(2):214-28. doi: 10.1002/prot.24178. Epub 2012 Sep 29.

PMID:
22965891
27.

Molecular determinants of selectivity and efficacy at the dopamine D3 receptor.

Newman AH, Beuming T, Banala AK, Donthamsetti P, Pongetti K, LaBounty A, Levy B, Cao J, Michino M, Luedtke RR, Javitch JA, Shi L.

J Med Chem. 2012 Aug 9;55(15):6689-99. doi: 10.1021/jm300482h. Epub 2012 Jun 7.

28.

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.

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

PMID:
22223256
29.

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

Goldfeld DA, Zhu K, Beuming T, Friesner RA.

Proc Natl Acad Sci U S A. 2011 May 17;108(20):8275-80. doi: 10.1073/pnas.1016951108. Epub 2011 May 2. Erratum in: Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9665.

30.

The binding sites for benztropines and dopamine in the dopamine transporter overlap.

Bisgaard H, Larsen MA, Mazier S, Beuming T, Newman AH, Weinstein H, Shi L, Loland CJ, Gether U.

Neuropharmacology. 2011 Jan;60(1):182-90. doi: 10.1016/j.neuropharm.2010.08.021. Epub 2010 Sep 6.

31.

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor.

Higgs C, Beuming T, Sherman W.

ACS Med Chem Lett. 2010 May 10;1(4):160-4. doi: 10.1021/ml100008s. eCollection 2010 Jul 8.

32.

Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD.

Thorsen TS, Madsen KL, Rebola N, Rathje M, Anggono V, Bach A, Moreira IS, Stuhr-Hansen N, Dyhring T, Peters D, Beuming T, Huganir R, Weinstein H, Mulle C, Strømgaard K, Rønn LC, Gether U.

Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):413-8. doi: 10.1073/pnas.0902225107. Epub 2009 Dec 14.

33.

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

Beuming T, Farid R, Sherman W.

Protein Sci. 2009 Aug;18(8):1609-19. doi: 10.1002/pro.177.

34.

The binding sites for cocaine and dopamine in the dopamine transporter overlap.

Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, Gether U, Loland CJ.

Nat Neurosci. 2008 Jul;11(7):780-9. doi: 10.1038/nn.2146. Epub 2008 Jun 22.

35.
36.

State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum.

Quick M, Yano H, Goldberg NR, Duan L, Beuming T, Shi L, Weinstein H, Javitch JA.

J Biol Chem. 2006 Sep 8;281(36):26444-54. Epub 2006 Jun 23.

37.

A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding.

Sen N, Shi L, Beuming T, Weinstein H, Javitch JA.

Neuropharmacology. 2005 Nov;49(6):780-90. Epub 2005 Oct 10.

PMID:
16216288
38.
39.

Molecular determinants for the complex binding specificity of the PDZ domain in PICK1.

Madsen KL, Beuming T, Niv MY, Chang CW, Dev KK, Weinstein H, Gether U.

J Biol Chem. 2005 May 27;280(21):20539-48. Epub 2005 Mar 17.

40.

PDZBase: a protein-protein interaction database for PDZ-domains.

Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H.

Bioinformatics. 2005 Mar;21(6):827-8. Epub 2004 Oct 28.

PMID:
15513994
41.

A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins.

Beuming T, Weinstein H.

Bioinformatics. 2004 Aug 12;20(12):1822-35. Epub 2004 Feb 26.

PMID:
14988128
42.

8R-lisuride is a potent stereospecific histamine H1-receptor partial agonist.

Bakker RA, Weiner DM, ter Laak T, Beuming T, Zuiderveld OP, Edelbroek M, Hacksell U, Timmerman H, Brann MR, Leurs R.

Mol Pharmacol. 2004 Mar;65(3):538-49. Erratum in: Mol Pharmacol. 2004 Apr;65(4):1048.

PMID:
14978232
43.

Probing conformational changes in neurotransmitter transporters: a structural context.

Goldberg NR, Beuming T, Soyer OS, Goldstein RA, Weinstein H, Javitch JA.

Eur J Pharmacol. 2003 Oct 31;479(1-3):3-12. Review.

PMID:
14612133

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