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 von 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

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Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein–Protein Interaction Interfaces von Ghanakota, Phani, van Vlijmen, Herman, Sherman, Woody, Beuming, Thijs

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What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands? von Michino, Mayako, Beuming, Thijs, Donthamsetti, Prashant, Newman, Amy Hauck, Javitch, Jonathan A, Shi, Lei

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Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization von Beuming, Thijs, Che, Ye, Abel, Robert, Kim, Byungchan, Shanmugasundaram, Veerabahu, Sherman, Woody

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Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia von 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.

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High‐energy water sites determine peptide binding affinity and specificity of PDZ domains von Beuming, Thijs, Farid, Ramy, Sherman, Woody

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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 Funct... von Beuming, Thijs, Shi, Lei, Javitch, Jonathan A, Weinstein, Harel

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

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Investigating Protein–Peptide Interactions Using the Schrödinger Computational Suite von Bhachoo, Jas, Beuming, Thijs

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

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Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors von Goldfeld, Dahlia A, Zhu, Kai, Beuming, Thijs, Friesner, Richard A

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PDZBase: a protein–protein interaction database for PDZ-domains von Beuming, Thijs, Skrabanek, Lucy, Niv, Masha Y., Mukherjee, Piali, Weinstein, Harel

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

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

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Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines von Beuming, Thijs, Sherman, Woody

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A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins von Beuming, Thijs, Weinstein, Harel

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Improved Docking of Polypeptides with Glide von Tubert-Brohman, Ivan, Sherman, Woody, Repasky, Matt, Beuming, Thijs

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State-dependent Conformations of the Translocation Pathway in the Tyrosine Transporter Tyt1, a Novel Neurotransmitter:Sodium Symporter from Fusobacterium nucleatum von Quick, Matthias, Yano, Hideaki, Goldberg, Naomi R., Duan, Lihua, Beuming, Thijs, Shi, Lei, Weinstein, Harel, Javitch, Jonathan A.

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Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger von 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

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Reply to Nikiforovich et al.: Restoration of the loop regions of G-protein–coupled receptors von Goldfeld, Dahlia A., Zhu, Kai, Beuming, Thijs, Friesner, Richard A.

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