| Year |
Citation |
Score |
| 2020 |
Cournia Z, Allen BK, Beuming T, Pearlman DA, Radak BK, Sherman W. Rigorous Free Energy Simulations in Virtual Screening. Journal of Chemical Information and Modeling. PMID 32539386 DOI: 10.1021/Acs.Jcim.0C00116 |
0.369 |
|
| 2019 |
Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, ... ... Beuming T, et al. Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nature Communications. 10: 2691. PMID 31217428 DOI: 10.1038/S41467-019-10523-3 |
0.348 |
|
| 2018 |
Ghanakota P, Van Vlijmen HWT, Sherman W, Beuming T. Large Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at PPI Interfaces. Journal of Chemical Information and Modeling. PMID 29617116 DOI: 10.1021/Acs.Jcim.7B00487 |
0.342 |
|
| 2018 |
Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Scientific Reports. 8: 720. PMID 29335433 DOI: 10.1038/S41598-017-18956-W |
0.349 |
|
| 2018 |
Tomasini MD, Wang Y, Karamafrooz A, Hall J, Taylor SS, Beuming T, Veglia G, Simon SM. Abstract 4142: Conformational dynamics of the chimeric kinase DNAJB1-PRKACA, the driver for fibrolamellar hepatocellular carcinoma Cancer Research. 78: 4142-4142. DOI: 10.1158/1538-7445.Am2018-4142 |
0.343 |
|
| 2017 |
Cappel D, Sherman W, Beuming T. Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery. Current Topics in Medicinal Chemistry. PMID 28413953 DOI: 10.2174/1568026617666170414141452 |
0.425 |
|
| 2017 |
Bhachoo J, Beuming T. Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite. Methods in Molecular Biology (Clifton, N.J.). 1561: 235-254. PMID 28236242 DOI: 10.1007/978-1-4939-6798-8_14 |
0.376 |
|
| 2016 |
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, et al. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. Acs Omega. 1: 293-304. PMID 30023478 DOI: 10.1021/acsomega.6b00086 |
0.345 |
|
| 2016 |
Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W. Relative Binding Free Energy Calculations Applied to Protein Homology Models. Journal of Chemical Information and Modeling. 56: 2388-2400. PMID 28024402 DOI: 10.1021/Acs.Jcim.6B00362 |
0.397 |
|
| 2016 |
Lenselink EB, Beuming T, van Veen C, Massink A, Sherman W, van Vlijmen HW, IJzerman AP. In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. Journal of Computer-Aided Molecular Design. PMID 27629350 DOI: 10.1007/S10822-016-9963-7 |
0.442 |
|
| 2016 |
McRobb FM, Negri A, Beuming T, Sherman W. Molecular dynamics techniques for modeling G protein-coupled receptors. Current Opinion in Pharmacology. 30: 69-75. PMID 27490828 DOI: 10.1016/J.Coph.2016.07.001 |
0.379 |
|
| 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 |
0.377 |
|
| 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 |
0.411 |
|
| 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 |
0.385 |
|
| 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 |
0.431 |
|
| 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 |
0.44 |
|
| 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 |
0.347 |
|
| 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 |
0.37 |
|
| 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 |
0.567 |
|
| 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 |
0.459 |
|
| 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 |
0.46 |
|
| 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 |
0.379 |
|
| 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 |
0.44 |
|
| 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 |
0.396 |
|
| 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 |
0.416 |
|
| 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 |
0.418 |
|
| 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 |
0.562 |
|
| 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 |
0.44 |
|
| 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 |
0.401 |
|
| 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 |
0.422 |
|
| 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 |
0.643 |
|
| 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 |
0.333 |
|
| 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: 160-4. PMID 24900189 DOI: 10.1021/Ml100008S |
0.421 |
|
| 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 |
0.618 |
|
| 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 |
0.411 |
|
| 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 |
0.381 |
|
| 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 |
0.539 |
|
| 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 |
0.558 |
|
| 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 |
0.55 |
|
| 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 |
0.59 |
|
| 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 |
0.537 |
|
| 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 |
0.584 |
|
| 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 |
0.513 |
|
| 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 |
0.522 |
|
| 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 |
0.542 |
|
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