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, Lingle, Wu, Yujie, Deng, Yuqing, Kim, Byungchan, Pierce, Levi, Krilov, Goran, Lupyan, Dmitry, Robinson, Shaughnessy, Dahlgren, Markus K, Greenwood, Jeremy, Romero, Donna L, Masse, Craig, Knight, Jennifer L, Steinbrecher, Thomas, Beuming, Thijs, Damm, Wolfgang, Harder, Ed, Sherman, Woody, Brewer, Mark, Wester, Ron, Murcko, Mark, Frye, Leah, Farid, Ramy, Lin, Teng, Mobley, David L, Jorgensen, William L, Berne, Bruce J, Friesner, Richard A, Abel, Robert
Published in Journal of the American Chemical Society (25.02.2015)
Published in Journal of the American Chemical Society (25.02.2015)
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Journal Article
Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
Beuming, Thijs, Che, Ye, Abel, Robert, Kim, Byungchan, Shanmugasundaram, Veerabahu, Sherman, Woody
Published in Proteins, structure, function, and bioinformatics (01.03.2012)
Published in Proteins, structure, function, and bioinformatics (01.03.2012)
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Journal Article
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Minuesa, Gerard, Albanese, Steven K., Xie, Wei, Kazansky, Yaniv, Worroll, Daniel, Chow, Arthur, Schurer, Alexandra, Park, Sun-Mi, Rotsides, Christina Z., Taggart, James, Rizzi, Andrea, Naden, Levi N., Chou, Timothy, Gourkanti, Saroj, Cappel, Daniel, Passarelli, Maria C., Fairchild, Lauren, Adura, Carolina, Glickman, J. Fraser, Schulman, Jessica, Famulare, Christopher, Patel, Minal, Eibl, Joseph K., Ross, Gregory M., Bhattacharya, Shibani, Tan, Derek S., Leslie, Christina S., Beuming, Thijs, Patel, Dinshaw J., Goldgur, Yehuda, Chodera, John D., Kharas, Michael G.
Published in Nature communications (19.06.2019)
Published in Nature communications (19.06.2019)
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Journal Article
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
Beuming, Thijs, Shi, Lei, Javitch, Jonathan A, Weinstein, Harel
Published in Molecular pharmacology (01.11.2006)
Published in Molecular pharmacology (01.11.2006)
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Journal Article
The binding sites for cocaine and dopamine in the dopamine transporter overlap
Javitch, Jonathan A, Loland, Claus J, Beuming, Thijs, Weinstein, Harel, Bergmann, Marianne L, Shi, Lei, Gether, Ulrik, Kniazeff, Julie, Raniszewska, Klaudia, Gracia, Luis, Newman, Amy Hauck
Published in Nature neuroscience (01.07.2008)
Published in Nature neuroscience (01.07.2008)
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Journal Article
Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins
Kamps, Jos J.A.G., Huang, Jiaxin, Poater, Jordi, Xu, Chao, Pieters, Bas J.G.E., Dong, Aiping, Min, Jinrong, Sherman, Woody, Beuming, Thijs, Matthias Bickelhaupt, F., Li, Haitao, Mecinović, Jasmin
Published in Nature communications (18.11.2015)
Published in Nature communications (18.11.2015)
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Journal Article
PDZBase: a protein–protein interaction database for PDZ-domains
Beuming, Thijs, Skrabanek, Lucy, Niv, Masha Y., Mukherjee, Piali, Weinstein, Harel
Published in Bioinformatics (15.03.2005)
Published in Bioinformatics (15.03.2005)
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Journal Article
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
Lenselink, Eelke B, Louvel, Julien, Forti, Anna F, van Veldhoven, Jacobus P. D, de Vries, Henk, Mulder-Krieger, Thea, McRobb, Fiona M, Negri, Ana, Goose, Joseph, Abel, Robert, van Vlijmen, Herman W. T, Wang, Lingle, Harder, Edward, Sherman, Woody, IJzerman, Adriaan P, Beuming, Thijs
Published in ACS omega (31.08.2016)
Published in ACS omega (31.08.2016)
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Journal Article
Identification of a small-molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD
Thorsen, Thor S, Madsen, Kenneth L, Rebola, Nelson, Rathje, Mette, Anggono, Victor, Bach, Anders, Moreira, Irina S, Stuhr-Hansen, Nicolai, Dyhring, Tino, Peters, Dan, Beuming, Thijs, Huganir, Richard, Weinstein, Harel, Mulle, Christophe, Strømgaard, Kristian, Rønn, Lars Christian B, Gether, Ulrik
Published in Proceedings of the National Academy of Sciences - PNAS (05.01.2010)
Published in Proceedings of the National Academy of Sciences - PNAS (05.01.2010)
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Journal Article
State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum
Quick, Matthias, Yano, Hideaki, Goldberg, Naomi R., Duan, Lihua, Beuming, Thijs, Shi, Lei, Weinstein, Harel, Javitch, Jonathan A.
Published in The Journal of biological chemistry (08.09.2006)
Published in The Journal of biological chemistry (08.09.2006)
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Journal Article
Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger
Pieters, Bas J. G. E., Wuts, Maud H. M., Poater, Jordi, Kumar, Kiran, White, Paul B., Kamps, Jos J. A. G., Sherman, Woody, Pruijn, Ger J. M., Paton, Robert S., Beuming, Thijs, Bickelhaupt, F. Matthias, Mecinović, Jasmin
Published in Communications chemistry (01.06.2020)
Published in Communications chemistry (01.06.2020)
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