Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations von Cournia, Zoe, Allen, Bryce, Sherman, Woody

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Rational Approaches to Improving Selectivity in Drug Design von Huggins, David J, Sherman, Woody, Tidor, Bruce

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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments von Madhavi Sastry, G., Adzhigirey, Matvey, Day, Tyler, Annabhimoju, Ramakrishna, Sherman, Woody

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Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field von Shivakumar, Devleena, Williams, Joshua, Wu, Yujie, Damm, Wolfgang, Shelley, John, Sherman, Woody

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Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis von Salam, Noeris K, Nuti, Roberto, Sherman, Woody

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Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes von Beard, Hege, Cholleti, Anuradha, Pearlman, David, Sherman, Woody, Loving, Kathryn A

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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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Predicting the Effect of Amino Acid Single-Point Mutations on Protein Stability—Large-Scale Validation of MD-Based Relative Free Energy Calculations von Steinbrecher, Thomas, Zhu, Chongkai, Wang, Lingle, Abel, Robert, Negron, Christopher, Pearlman, David, Feyfant, Eric, Duan, Jianxin, Sherman, Woody

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Water Networks Contribute to Enthalpy/Entropy Compensation in Protein–Ligand Binding von Breiten, Benjamin, Lockett, Matthew R, Sherman, Woody, Fujita, Shuji, Al-Sayah, Mohammad, Lange, Heiko, Bowers, Carleen M, Heroux, Annie, Krilov, Goran, Whitesides, George M

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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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Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics von Kimura, S. Roy, Hu, Hai Peng, Ruvinsky, Anatoly M, Sherman, Woody, Favia, Angelo D

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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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Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments von Sastry, Madhavi, Lowrie, Jeffrey F, Dixon, Steven L, Sherman, Woody

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Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones von Nordquist, Erik B, English, Charles A, Clerico, Eugenia M, Sherman, Woody, Gierasch, Lila M, Chen, Jianhan

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Structure-based approach to the prediction of disulfide bonds in proteins von Salam, Noeris K., Adzhigirey, Matvey, Sherman, Woody, Pearlman, David A.

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Accurate Binding Free Energy Predictions in Fragment Optimization von Steinbrecher, Thomas B, Dahlgren, Markus, Cappel, Daniel, Lin, Teng, Wang, Lingle, Krilov, Goran, Abel, Robert, Friesner, Richard, Sherman, Woody

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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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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers von Watts, K. Shawn, Dalal, Pranav, Murphy, Robert B, Sherman, Woody, Friesner, Rich A, Shelley, John C

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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry von Dixon, Tom, MacPherson, Derek, Mostofian, Barmak, Dauzhenka, Taras, Lotz, Samuel, McGee, Dwight, Shechter, Sharon, Shrestha, Utsab R., Wiewiora, Rafal, McDargh, Zachary A., Pei, Fen, Pal, Rajat, Ribeiro, João V., Wilkerson, Tanner, Sachdeva, Vipin, Gao, Ning, Jain, Shourya, Sparks, Samuel, Li, Yunxing, Vinitsky, Alexander, Zhang, Xin, Razavi, Asghar M., Kolossváry, István, Imbriglio, Jason, Evdokimov, Artem, Bergeron, Louise, Zhou, Wenchang, Adhikari, Jagat, Ruprecht, Benjamin, Dickson, Alex, Xu, Huafeng, Sherman, Woody, Izaguirre, Jesus A.

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Mechanism of the hydrophobic effect in the biomolecular recognition of arylsulfonamides by carbonic anhydrase von Snyder, Phillip W, Mecinović, Jasmin, Moustakas, Demetri T, Thomas, Samuel W. III, Harder, Michael, Mack, Eric T, Lockett, Matthew R, Héroux, Annie, Sherman, Woody, Whitesides, George M

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