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Thijs Beuming
Thijs Beuming
Latham Biopharm Group
Verified email at lathambiopharm.com
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Cited by
Year
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
L Wang, Y Wu, Y Deng, B Kim, L Pierce, G Krilov, D Lupyan, S Robinson, ...
Journal of the American Chemical Society 137 (7), 2695-2703, 2015
10862015
The binding sites for cocaine and dopamine in the dopamine transporter overlap
T Beuming, J Kniazeff, ML Bergmann, L Shi, L Gracia, K Raniszewska, ...
Nature neuroscience 11 (7), 780-789, 2008
4102008
A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and …
T Beuming, L Shi, JA Javitch, H Weinstein
Molecular pharmacology 70 (5), 1630-1642, 2006
3202006
PDZBase: a protein–protein interaction database for PDZ-domains
T Beuming, L Skrabanek, MY Niv, P Mukherjee, H Weinstein
Bioinformatics 21 (6), 827-828, 2005
2442005
Improved docking of polypeptides with Glide
I Tubert-Brohman, W Sherman, M Repasky, T Beuming
Journal of chemical information and modeling 53 (7), 1689-1699, 2013
1872013
Molecular determinants of selectivity and efficacy at the dopamine D3 receptor
AH Newman, T Beuming, AK Banala, P Donthamsetti, K Pongetti, ...
Journal of medicinal chemistry 55 (15), 6689-6699, 2012
1862012
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
T Beuming, Y Che, R Abel, B Kim, V Shanmugasundaram, W Sherman
Proteins: Structure, Function, and Bioinformatics 80 (3), 871-883, 2012
1652012
High‐energy water sites determine peptide binding affinity and specificity of PDZ domains
T Beuming, R Farid, W Sherman
Protein Science 18 (8), 1609-1619, 2009
1402009
Rigorous free energy simulations in virtual screening
Z Cournia, BK Allen, T Beuming, DA Pearlman, BK Radak, W Sherman
Journal of chemical information and modeling 60 (9), 4153-4169, 2020
1382020
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD
TS Thorsen, KL Madsen, N Rebola, M Rathje, V Anggono, A Bach, ...
Proceedings of the National Academy of Sciences 107 (1), 413-418, 2010
1372010
What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?
M Michino, T Beuming, P Donthamsetti, AH Newman, JA Javitch, L Shi
Pharmacological Reviews 67 (1), 198-213, 2015
1202015
Predicting binding affinities for GPCR ligands using free-energy perturbation
EB Lenselink, J Louvel, AF Forti, JPD van Veldhoven, H de Vries, ...
ACS omega 1 (2), 293-304, 2016
1182016
Investigating protein–peptide interactions using the Schrödinger computational suite
J Bhachoo, T Beuming
Modeling peptide-protein interactions: methods and protocols, 235-254, 2017
1172017
Hydration site thermodynamics explain SARs for triazolylpurines analogues binding to the A2A receptor
C Higgs, T Beuming, W Sherman
ACS medicinal chemistry letters 1 (4), 160-164, 2010
1172010
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
G Minuesa, SK Albanese, W Xie, Y Kazansky, D Worroll, A Chow, ...
Nature communications 10 (1), 2691, 2019
1162019
Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines
T Beuming, W Sherman
Journal of chemical information and modeling 52 (12), 3263-3277, 2012
1062012
Ligand-Dependent Activation and Deactivation of the Human Adenosine A2A Receptor
J Li, AL Jonsson, T Beuming, JC Shelley, GA Voth
Journal of the American Chemical Society 135 (23), 8749-8759, 2013
1052013
Molecular determinants for the complex binding specificity of the PDZ domain in PICK1
KL Madsen, T Beuming, MY Niv, C Chang, KK Dev, H Weinstein, ...
Journal of Biological Chemistry 280 (21), 20539-20548, 2005
1042005
State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter: sodium symporter from Fusobacterium nucleatum
M Quick, H Yano, NR Goldberg, L Duan, T Beuming, L Shi, H Weinstein, ...
Journal of biological chemistry 281 (36), 26444-26454, 2006
1022006
Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter
P Plenge, L Shi, T Beuming, J Te, AH Newman, H Weinstein, U Gether, ...
Journal of Biological Chemistry 287 (47), 39316-39326, 2012
922012
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