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2020 – today
- 2024
[j39]Lieyang Chen, Yujie Wu, Chuanjie Wu, Ana Silveira, Woody Sherman
, Huafeng Xu, Emilio Gallicchio:
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands. J. Chem. Inf. Model. 64(1): 250-264 (2024)- [j38]Albert Bou, Morgan Thomas, Sebastian Dittert, Carles Navarro, Maciej Majewski, Ye Wang, Shivam Patel, Gary Tresadern, Mazen Ahmad, Vincent Moens, Woody Sherman, Simone Sciabola, Gianni De Fabritiis:
ACEGEN: Reinforcement Learning of Generative Chemical Agents for Drug Discovery. J. Chem. Inf. Model. 64(15): 5900-5911 (2024) - [i2]Albert Bou, Morgan 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:
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery. CoRR abs/2405.04657 (2024) - 2023
- [j37]Barmak Mostofian, Holli-Joi Martin, Asghar Razavi, Shivam Patel, Bryce K. Allen, Woody Sherman, Jesus A. Izaguirre:
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods. J. Chem. Inf. Model. 63(17): 5408-5432 (2023) - 2022
- [c6]Chunshu Wu, Sahan Bandara, Tong Geng, Anqi Guo, Pouya Haghi, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
Optimized Mappings for Symmetric Range-Limited Molecular Force Calculations on FPGAs. FPL 2022: 101-108 - 2021
- [j36]Erik B. Nordquist, Charles A. English, Eugenia M. Clerico, Woody Sherman, Lila M. Gierasch, Jianhan Chen:
Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. PLoS Comput. Biol. 17(11) (2021) - [c5]Chunshu Wu, Tong Geng, Sahan Bandara, Chen Yang, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
Upgrade of FPGA Range-Limited Molecular Dynamics to Handle Hundreds of Processors. FCCM 2021: 142-151 - [c4]Chunshu Wu, Sahan Bandara, Tong Geng, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
System-Level Modeling of GPU/FPGA Clusters for Molecular Dynamics Simulations. HPEC 2021: 1-8 - 2020
- [j35]Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, Woody Sherman:
Rigorous Free Energy Simulations in Virtual Screening. J. Chem. Inf. Model. 60(9): 4153-4169 (2020) - [j34]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:
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. J. Chem. Inf. Model. 60(11): 5595-5623 (2020) - [c3]Chunshu Wu, Tong Geng, Chen Yang, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics. HPEC 2020: 1-8
2010 – 2019
- 2019
- [c2]Chen Yang, Tong Geng, Tianqi Wang, Charles Lin, Jiayi Sheng, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
Molecular Dynamics Range-Limited Force Evaluation Optimized for FPGAs. ASAP 2019: 263-271 - [c1]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:
Fully integrated FPGA molecular dynamics simulations. SC 2019: 67:1-67:31 - [i1]Chen Yang, Tong Geng, Tianqi Wang, Rushi Patel, Qingqing Xiong, Ahmed Sanaullah, Jiayi Sheng, Charles Lin, Vipin Sachdeva, Woody Sherman, Martin C. Herbordt:
Fully Integrated On-FPGA Molecular Dynamics Simulations. CoRR abs/1905.05359 (2019) - 2018
- [j33]Phani Ghanakota, Herman van Vlijmen, Woody Sherman, Thijs Beuming:
Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. J. Chem. Inf. Model. 58(4): 784-793 (2018) - 2017
- [j32]S. Roy Kimura, Hai Peng Hu, Anatoly M. Ruvinsky, Woody Sherman, Angelo D. Favia:
Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics. J. Chem. Inf. Model. 57(6): 1388-1401 (2017) - [j31]Zoe Cournia, Bryce K. Allen, Woody Sherman:
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J. Chem. Inf. Model. 57(12): 2911-2937 (2017) - 2016
- [j30]Eelke B. Lenselink, Thijs Beuming, Corine van Veen, Arnault Massink, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman:
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. J. Comput. Aided Mol. Des. 30(10): 863-874 (2016) - [j29]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:
Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules. J. Comput. Chem. 37(16): 1425-1441 (2016) - [j28]Daniel Robinson, Thomas Bertrand, Jean-Christophe Carry, Frank Halley, Andreas Karlsson, Magali Mathieu, Hervé Minoux, Marc-Antoine Perrin, Benoit Robert, Laurent Schio, Woody Sherman:
Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications. J. Chem. Inf. Model. 56(5): 886-894 (2016) - [j27]Michelle Lynn Hall, David Calkins, Woody Sherman:
Automated Protocol for Large-Scale Modeling of Gene Expression Data. J. Chem. Inf. Model. 56(11): 2216-2224 (2016) - [j26]Daniel Cappel, Michelle Lynn Hall, Eelke B. Lenselink, Thijs Beuming, Jun Qi, James Bradner, Woody Sherman:
Relative Binding Free Energy Calculations Applied to Protein Homology Models. J. Chem. Inf. Model. 56(12): 2388-2400 (2016) - 2015
- [j25]Daniel Cappel, Steven L. Dixon, Woody Sherman, Jianxin Duan:
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. J. Comput. Aided Mol. Des. 29(2): 165-182 (2015) - [j24]Thomas B. Steinbrecher, Markus K. Dahlgren, Daniel Cappel, Teng Lin, Lingle Wang, Goran Krilov, Robert Abel, Richard A. Friesner, Woody Sherman:
Accurate Binding Free Energy Predictions in Fragment Optimization. J. Chem. Inf. Model. 55(11): 2411-2420 (2015) - 2014
- [j23]Daniel Cappel, Vassilios Myrianthopoulos, Emmanuel Mikros, Woody Sherman:
Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases. J. Cheminformatics 6(S-1): 6 (2014) - [j22]Anat Levit, Thijs Beuming, Goran Krilov, Woody Sherman, Masha Y. Niv:
Predicting GPCR Promiscuity Using Binding Site Features. J. Chem. Inf. Model. 54(1): 184-194 (2014) - [j21]Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman:
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor. J. Chem. Inf. Model. 54(6): 1737-1746 (2014) - [j20]Sarah Sirin, Rajesh Kumar, Carlos Martínez, Michael J. Karmilowicz, Preeyantee Ghosh, Yuriy A. Abramov, Van Martin, Woody Sherman:
A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring. J. Chem. Inf. Model. 54(8): 2334-2346 (2014) - [j19]Paulette A. Greenidge, Christian Kramer, Jean-Christophe Mozziconacci, Woody Sherman:
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. J. Chem. Inf. Model. 54(10): 2697-2717 (2014) - 2013
- [j18]G. Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman:
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J. Comput. Aided Mol. Des. 27(3): 221-234 (2013) - [j17]Dmitry Lupyan, Yuriy A. Abramov, Woody Sherman:
Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J. Comput. Aided Mol. Des. 27(3): 293 (2013) - [j16]Daniele Pala, Thijs Beuming, Woody Sherman, Alessio Lodola, Silvia Rivara, Marco Mor:
Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement. J. Chem. Inf. Model. 53(4): 821-835 (2013) - [j15]G. Madhavi Sastry, V. S. Sandeep Inakollu, Woody Sherman:
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking. J. Chem. Inf. Model. 53(7): 1531-1542 (2013) - [j14]Ivan Tubert-Brohman, Woody Sherman, Matthew P. Repasky, Thijs Beuming:
Improved Docking of Polypeptides with Glide. J. Chem. Inf. Model. 53(7): 1689-1699 (2013) - [j13]Yuling An, Woody Sherman, Steven L. Dixon:
Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization. J. Chem. Inf. Model. 53(9): 2312-2321 (2013) - 2012
- [j12]Dmitry Lupyan, Yuriy A. Abramov, Woody Sherman:
Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J. Comput. Aided Mol. Des. 26(11): 1195-1205 (2012) - [j11]Ori Kalid, Dora Toledo Warshaviak, Sharon Shechter, Woody Sherman, Sharon Shacham:
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors. J. Comput. Aided Mol. Des. 26(11): 1217-1228 (2012) - [j10]Falgun Shah, Jiri Gut, Jennifer Legac, Devleena Shivakumar, Woody Sherman, Philip J. Rosenthal, Mitchell A. Avery:
Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis. J. Chem. Inf. Model. 52(3): 696-710 (2012) - [j9]Thijs Beuming, Woody Sherman:
Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines. J. Chem. Inf. Model. 52(12): 3263-3277 (2012) - 2011
- [j8]Jianxin Duan, G. Madhavi Sastry, Steven L. Dixon, Jeffrey F. Lowrie, Woody Sherman:
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods. J. Cheminformatics 3(S-1): 1 (2011) - [j7]Kathryn Loving, Noeris K. Salam, Daniel Cappel, Woody Sherman:
Generation of structure-based pharmacophores using energetic analysis - application on fragment docking. J. Cheminformatics 3(S-1): 20 (2011) - [j6]G. Madhavi Sastry, Steven L. Dixon, Woody Sherman:
Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring. J. Chem. Inf. Model. 51(10): 2455-2466 (2011) - 2010
- [j5]K. Shawn Watts, Pranav Dalal, Robert B. Murphy, Woody Sherman, Richard A. Friesner, John C. Shelley:
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. J. Chem. Inf. Model. 50(4): 534-546 (2010) - [j4]G. Madhavi Sastry, Jeffrey F. Lowrie, Steven L. Dixon, Woody Sherman:
Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments. J. Chem. Inf. Model. 50(5): 771-784 (2010)
2000 – 2009
- 2009
- [j3]Kathryn Loving, Noeris K. Salam, Woody Sherman:
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. J. Comput. Aided Mol. Des. 23(8): 541-554 (2009) - [j2]Noeris K. Salam, Roberto Nuti, Woody Sherman:
Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis. J. Chem. Inf. Model. 49(10): 2356-2368 (2009) - 2008
- [j1]Shashidhar N. Rao, Paul C. Sanschagrin, Jeremy R. Greenwood, Matthew P. Repasky, Woody Sherman, Ramy Farid:
Improving database enrichment through ensemble docking. J. Comput. Aided Mol. Des. 22(9): 621-627 (2008)
Coauthor Index
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