Thijs Beuming - Publications

Affiliations: 
Application Science Schrodinger 
Area:
Computational Chemistry
Website:
http://www.schrodinger.com

39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Beuming T, Shi L. Editorial: Computer Aided Structure-based Lead Optimization. Current Topics in Medicinal Chemistry. 17: 2575-2576. PMID 28889794 DOI: 10.2174/156802661723170808161306  0.48
2015 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. Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins. Nature Communications. 6: 8911. PMID 26578293 DOI: 10.1038/ncomms9911  1
2015 Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W. Docking and Virtual Screening Strategies for GPCR Drug Discovery. Methods in Molecular Biology (Clifton, N.J.). 1335: 251-76. PMID 26260606 DOI: 10.1007/978-1-4939-2914-6_17  1
2015 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, et al. 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. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/ja512751q  1
2015 Michino M, Beuming T, Donthamsetti P, Newman AH, Javitch JA, Shi L. What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands? Pharmacological Reviews. 67: 198-213. PMID 25527701 DOI: 10.1124/pr.114.009944  0.48
2015 Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor. The Journal of Physical Chemistry. B. 119: 824-35. PMID 25395044 DOI: 10.1021/jp5053612  1
2014 Kufareva I, Katritch V, Stevens RC, Abagyan R. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure (London, England : 1993). 22: 1120-39. PMID 25066135 DOI: 10.1016/j.str.2014.06.012  1
2014 Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP. Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor. Journal of Chemical Information and Modeling. 54: 1737-46. PMID 24835542 DOI: 10.1021/ci5000455  1
2014 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, ... ... Beuming T, et al. Discovery and characterization of a G protein-biased agonist that inhibits β-arrestin recruitment to the D2 dopamine receptor. Molecular Pharmacology. 86: 96-105. PMID 24755247 DOI: 10.1124/mol.113.090563  1
2014 Dehnes Y, Shan J, Beuming T, Shi L, Weinstein H, Javitch JA. Conformational changes in dopamine transporter intracellular regions upon cocaine binding and dopamine translocation. Neurochemistry International. 73: 4-15. PMID 24576496 DOI: 10.1016/j.neuint.2014.02.003  1
2014 Levit A, Beuming T, Krilov G, Sherman W, Niv MY. Predicting GPCR promiscuity using binding site features Journal of Chemical Information and Modeling. 54: 184-194. PMID 24328091 DOI: 10.1021/ci400552z  1
2013 Michino M, Donthamsetti P, Beuming T, Banala A, Duan L, Roux T, Han Y, Trinquet E, Newman AH, Javitch JA, Shi L. A single glycine in extracellular loop 1 is the critical determinant for pharmacological specificity of dopamine D2 and D3 receptors. Molecular Pharmacology. 84: 854-64. PMID 24061855 DOI: 10.1124/mol.113.087833  1
2013 Tubert-Brohman I, Sherman W, Repasky M, Beuming T. Improved docking of polypeptides with glide Journal of Chemical Information and Modeling. 53: 1689-1699. PMID 23800267 DOI: 10.1021/ci400128m  1
2013 Li J, Jonsson AL, Beuming T, Shelley JC, Voth GA. Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor. Journal of the American Chemical Society. 135: 8749-59. PMID 23678995 DOI: 10.1021/ja404391q  1
2013 Pala D, Beuming T, Sherman W, Lodola A, Rivara S, Mor M. Structure-based virtual screening of MT2 melatonin receptor: Influence of template choice and structural refinement Journal of Chemical Information and Modeling. 53: 821-835. PMID 23541165 DOI: 10.1021/ci4000147  1
2013 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Loop prediction for a GPCR homology model: algorithms and results. Proteins. 81: 214-28. PMID 22965891 DOI: 10.1002/prot.24178  1
2012 Beuming T, Sherman W. Current assessment of docking into GPCR crystal structures and homology models: Successes, challenges, and guidelines Journal of Chemical Information and Modeling. 52: 3263-3277. PMID 23121495 DOI: 10.1021/ci300411b  1
2012 Plenge P, Shi L, Beuming T, Te J, Newman AH, Weinstein H, Gether U, Loland CJ. Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter. The Journal of Biological Chemistry. 287: 39316-26. PMID 23007398 DOI: 10.1074/jbc.M112.371765  1
2012 Newman AH, Beuming T, Banala AK, Donthamsetti P, Pongetti K, LaBounty A, Levy B, Cao J, Michino M, Luedtke RR, Javitch JA, Shi L. Molecular determinants of selectivity and efficacy at the dopamine D3 receptor. Journal of Medicinal Chemistry. 55: 6689-99. PMID 22632094 DOI: 10.1021/jm300482h  1
2012 Beuming T, Che Y, Abel R, Kim B, Shanmugasundaram V, Sherman W. Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization. Proteins. 80: 871-83. PMID 22223256 DOI: 10.1002/prot.23244  1
2012 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 20 (8275-8280) 10.1073/pnas.1016951108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9665. DOI: 10.1073/pnas.1207511109  1
2011 Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England : 1993). 19: 1108-26. PMID 21827947 DOI: 10.1016/j.str.2011.05.012  1
2011 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America. 108: 8275-80. PMID 21536915 DOI: 10.1073/pnas.1016951108  1
2011 Bisgaard H, Larsen MA, Mazier S, Beuming T, Newman AH, Weinstein H, Shi L, Loland CJ, Gether U. The binding sites for benztropines and dopamine in the dopamine transporter overlap. Neuropharmacology. 60: 182-90. PMID 20816875 DOI: 10.1016/j.neuropharm.2010.08.021  1
2011 Goldfeld DA, Zhu K, Beuming T, Friesner RA. Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein-coupled receptors Proceedings of the National Academy of Sciences of the United States of America. 108: E342. DOI: 10.1073/pnas.1108089108  1
2010 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, et al. Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD. Proceedings of the National Academy of Sciences of the United States of America. 107: 413-8. PMID 20018661 DOI: 10.1073/pnas.0902225107  1
2010 Shi L, Srdanovic M, Beuming T, Skrabanek L, Javitch JA, Weinstein H. TRAC - A platform for structure-function studies of NSS-proteins integrates information from bioinformatics and biomedical literature 10th Ieee International Conference On Bioinformatics and Bioengineering 2010, Bibe 2010. 267-272. DOI: 10.1109/BIBE.2010.51  1
2010 Higgs C, Beuming T, Sherman W. Hydration site thermodynamics explain SARs for triazolylpurines analogues binding to the A2A receptor Acs Medicinal Chemistry Letters. 1: 160-164. DOI: 10.1021/ml100008s  1
2009 Beuming T, Farid R, Sherman W. High-energy water sites determine peptide binding affinity and specificity of PDZ domains Protein Science. 18: 1609-1619. PMID 19569188 DOI: 10.1002/pro.177  1
2008 Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, Gether U, Loland CJ. The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nature Neuroscience. 11: 780-9. PMID 18568020 DOI: 10.1038/nn.2146  1
2006 Beuming T, Shi L, Javitch JA, Weinstein H. 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 function. Molecular Pharmacology. 70: 1630-42. PMID 16880288 DOI: 10.1124/mol.106.026120  1
2006 Quick M, Yano H, Goldberg NR, Duan L, Beuming T, Shi L, Weinstein H, Javitch JA. State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum. The Journal of Biological Chemistry. 281: 26444-54. PMID 16798738 DOI: 10.1074/jbc.M602438200  1
2005 Sen N, Shi L, Beuming T, Weinstein H, Javitch JA. A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding. Neuropharmacology. 49: 780-90. PMID 16216288 DOI: 10.1016/j.neuropharm.2005.08.014  1
2005 Beuming T, Weinstein H. Modeling membrane proteins based on low-resolution electron microscopy maps: A template for the TM domains of the oxalate transporter OxIT Protein Engineering, Design and Selection. 18: 119-125. PMID 15820982 DOI: 10.1093/protein/gzi013  1
2005 Madsen KL, Beuming T, Niv MY, Chang CW, Dev KK, Weinstein H, Gether U. Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. The Journal of Biological Chemistry. 280: 20539-48. PMID 15774468 DOI: 10.1074/jbc.M500577200  1
2005 Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: A protein-protein interaction database for PDZ-domains Bioinformatics. 21: 827-828. PMID 15513994 DOI: 10.1093/bioinformatics/bti098  1
2004 Beuming T, Weinstein H. A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins Bioinformatics. 20: 1822-1835. PMID 14988128 DOI: 10.1093/bioinformatics/bth143  1
2004 Bakker RA, Weiner DM, ter Laak T, Beuming T, Zuiderveld OP, Edelbroek M, Hacksell U, Timmerman H, Brann MR, Leurs R. 8R-lisuride is a potent stereospecific histamine H1-receptor partial agonist. Molecular Pharmacology. 65: 538-49. PMID 14978232 DOI: 10.1124/mol.65.3.538  1
2003 Goldberg NR, Beuming T, Soyer OS, Goldstein RA, Weinstein H, Javitch JA. Probing conformational changes in neurotransmitter transporters: a structural context. European Journal of Pharmacology. 479: 3-12. PMID 14612133 DOI: 10.1016/j.ejphar.2003.08.052  1
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