Woody Sherman - RankMe

49 papers A 1B 1Misc 1Journal 43Unranked 3

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling. J. Chem. Inf. Model. Karmen Condic-Jurkic, Irfan Alibay, Woody Sherman, Mallory R. Tollefson, W. Patrick Walters, Zachary Baker, Lillian T. Chong, Jennifer N. Wei, Jeffrey J. Gray, Brian D. Weitzner, Daniel G. A. Smith, Julia Koehler Leman, Chris Bahl, David L. Mobley
2025	J	`jnl`	In Search of Beautiful Molecules: A Perspective on Generative Modeling for Drug Design. J. Chem. Inf. Model. Remco L. van den Broek, Shivam Patel, Gerard J. P. van Westen, Willem Jespers, Woody Sherman
2024	J	`jnl`	ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. J. Chem. Inf. Model. Albert Bou, Morgan C. Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis
2024	J	`jnl`	ACEGEN: Reinforcement learning of generative chemical agents for drug discovery. CoRR Albert Bou, Morgan C. Thomas, Sebastian Dittert, Carles Navarro Ramírez, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis
2024	J	`jnl`	Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. J. Chem. Inf. Model. Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman, Huafeng Xu, Emilio Gallicchio
2023	J	`jnl`	Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J. Chem. Inf. Model. Barmak Mostofian, Holli-Joi Martin, Asghar Razavi, Shivam Patel, Bryce K. Allen, Woody Sherman, Jesus A. Izaguirre
2022	B	`conf`	Optimized Mappings for Symmetric Range-Limited Molecular Force Calculations on FPGAs. FPL Chunshu Wu, Sahan Bandara, Tong Geng, Anqi Guo, Pouya Haghi, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2021	J	`jnl`	Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. PLoS Comput. Biol. Erik B. Nordquist, Charles A. English, Eugenia M. Clerico, Woody Sherman, Lila M. Gierasch, Jianhan Chen
2021	—	`conf`	System-Level Modeling of GPU/FPGA Clusters for Molecular Dynamics Simulations. HPEC Chunshu Wu, Sahan Bandara, Tong Geng, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2021	Misc	`conf`	Upgrade of FPGA Range-Limited Molecular Dynamics to Handle Hundreds of Processors. FCCM Chunshu Wu, Tong Geng, Sahan Bandara, Chen Yang, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2020	—	`conf`	A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics. HPEC Chunshu Wu, Tong Geng, Chen Yang, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2020	J	`jnl`	Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. J. Chem. Inf. Model. Tai-Sung Lee, Bryce K. Allen, Timothy J. Giese, Zhenyu Guo, Pengfei Li, Charles Lin, T. Dwight McGee Jr., David A. Pearlman, Brian K. Radak, Yujun Tao, Hsu-Chun Tsai, Huafeng Xu, Woody Sherman, Darrin M. York
2020	J	`jnl`	Rigorous Free Energy Simulations in Virtual Screening. J. Chem. Inf. Model. Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, Woody Sherman
2019	J	`jnl`	Fully Integrated On-FPGA Molecular Dynamics Simulations. CoRR Chen Yang, Tong Geng, Tianqi Wang, Rushi Patel, Qingqing Xiong, Ahmed Sanaullah, Jiayi Sheng, Charles Lin, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2019	A	`conf`	Fully integrated FPGA molecular dynamics simulations. SC Chen Yang, Tong Geng, Tianqi Wang, Rushi Patel, Qingqing Xiong, Ahmed Sanaullah, Chunshu Wu, Jiayi Sheng, Charles Lin, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2019	—	`conf`	Molecular Dynamics Range-Limited Force Evaluation Optimized for FPGAs. ASAP Chen Yang, Tong Geng, Tianqi Wang, Charles Lin, Jiayi Sheng, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt
2018	J	`jnl`	Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. J. Chem. Inf. Model. Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming
2017	J	`jnl`	Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. S. Roy Kimura, Hai Peng Hu, Anatoly M. Ruvinsky, Woody Sherman, Angelo D. Favia
2017	J	`jnl`	Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J. Chem. Inf. Model. Zoe Cournia, Bryce K. Allen, Woody Sherman
2016	J	`jnl`	Automated Protocol for Large-Scale Modeling of Gene Expression Data. J. Chem. Inf. Model. Michelle Lynn Hall, David Calkins, Woody Sherman
2016	J	`jnl`	Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications. J. Chem. Inf. Model. Daniel Robinson, Thomas Bertrand, Jean-Christophe Carry, Frank Halley, Andreas Karlsson, Magali Mathieu, Hervé Minoux, Marc-Antoine Perrin, Benoit Robert, Laurent Schio, Woody Sherman
2016	J	`jnl`	Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules. J. Comput. Chem. Yixiang X. Cao, Thomas Hughes, Dave Giesen, Mathew D. Halls, Alexander Goldberg, Tati Reddy Vadicherla, G. Madhavi Sastry, Bhargav Patel, Woody Sherman, Andrew L. Weisman, Richard A. Friesner
2016	J	`jnl`	In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. J. Comput. Aided Mol. Des. Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
2016	J	`jnl`	Relative Binding Free Energy Calculations Applied to Protein Homology Models. J. Chem. Inf. Model. Daniel Cappel, Michelle Lynn Hall, Eelke B. Lenselink, Thijs Beuming, Jun Qi, James Bradner, Woody Sherman
2015	J	`jnl`	Accurate Binding Free Energy Predictions in Fragment Optimization. J. Chem. Inf. Model. Thomas B. Steinbrecher, Markus K. Dahlgren, Daniel Cappel, Teng Lin, Lingle Wang, Goran Krilov, Robert Abel, Richard A. Friesner, Woody Sherman
2015	J	`jnl`	Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. J. Comput. Aided Mol. Des. Daniel Cappel, Steven L. Dixon, Woody Sherman, Jianxin Duan
2014	J	`jnl`	A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring. J. Chem. Inf. Model. Sarah Sirin, Rajesh Kumar, Carlos Martínez, Michael J. Karmilowicz, Preeyantee Ghosh, Yuriy A. Abramov, Van Martin, Woody Sherman
2014	J	`jnl`	Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases. J. Cheminformatics Daniel Cappel, Vassilios Myrianthopoulos, Emmanuel Mikros, Woody Sherman
2014	J	`jnl`	Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. J. Chem. Inf. Model. Paulette A. Greenidge, Christian Kramer, Jean-Christophe Mozziconacci, Woody Sherman
2014	J	`jnl`	Predicting GPCR Promiscuity Using Binding Site Features. J. Chem. Inf. Model. Anat Levit, Thijs Beuming, Goran Krilov, Woody Sherman, Masha Y. Niv
2014	J	`jnl`	Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A J. Chem. Inf. Model. Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman
2013	J	`jnl`	Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. J. Chem. Inf. Model. G. Madhavi Sastry, V. S. Sandeep Inakollu, Woody Sherman
2013	J	`jnl`	Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J. Comput. Aided Mol. Des. Dmitry Lupyan, Yuriy A. Abramov, Woody Sherman
2013	J	`jnl`	Improved Docking of Polypeptides with Glide. J. Chem. Inf. Model. Ivan Tubert-Brohman, Woody Sherman, Matthew P. Repasky, Thijs Beuming
2013	J	`jnl`	Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization. J. Chem. Inf. Model. Yuling An, Woody Sherman, Steven L. Dixon
2013	J	`jnl`	Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des. G. Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman
2013	J	`jnl`	Structure-Based Virtual Screening of MT J. Chem. Inf. Model. Daniele Pala, Thijs Beuming, Woody Sherman, Alessio Lodola, Silvia Rivara, Marco Mor
2012	J	`jnl`	Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J. Comput. Aided Mol. Des. Dmitry Lupyan, Yuriy A. Abramov, Woody Sherman
2012	J	`jnl`	Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis. J. Chem. Inf. Model. Falgun Shah, Jiri Gut, Jennifer Legac, Devleena Shivakumar, Woody Sherman, Philip J. Rosenthal, Mitchell A. Avery
2012	J	`jnl`	Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J. Comput. Aided Mol. Des. Ori Kalid, Dora Toledo Warshaviak, Sharon Shechter, Woody Sherman, Sharon Shacham
2012	J	`jnl`	Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines. J. Chem. Inf. Model. Thijs Beuming, Woody Sherman
2011	J	`jnl`	Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J. Cheminformatics Jianxin Duan, G. Madhavi Sastry, Steven L. Dixon, Jeffrey F. Lowrie, Woody Sherman
2011	J	`jnl`	Generation of structure-based pharmacophores using energetic analysis - application on fragment docking. J. Cheminformatics Kathryn Loving, Noeris K. Salam, Daniel Cappel, Woody Sherman
2011	J	`jnl`	Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring. J. Chem. Inf. Model. G. Madhavi Sastry, Steven L. Dixon, Woody Sherman
2010	J	`jnl`	ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. J. Chem. Inf. Model. K. Shawn Watts, Pranav Dalal, Robert B. Murphy, Woody Sherman, Richard A. Friesner, John C. Shelley
2010	J	`jnl`	Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments. J. Chem. Inf. Model. G. Madhavi Sastry, Jeffrey F. Lowrie, Steven L. Dixon, Woody Sherman
2009	J	`jnl`	Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. J. Comput. Aided Mol. Des. Kathryn Loving, Noeris K. Salam, Woody Sherman
2009	J	`jnl`	Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis. J. Chem. Inf. Model. Noeris K. Salam, Roberto Nuti, Woody Sherman
2008	J	`jnl`	Improving database enrichment through ensemble docking. J. Comput. Aided Mol. Des. Shashidhar N. Rao, Paul C. Sanschagrin, Jeremy R. Greenwood, Matthew P. Repasky, Woody Sherman, Ramy Farid