Woody Sherman
Orcid: 0000-0001-9079-1376
According to our database1,
Woody Sherman
authored at least 45 papers
between 2008 and 2024.
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Bibliography
2024
Performance and Analysis of the Alchemical Transfer Method for Binding-Free-Energy Predictions of Diverse Ligands.
J. Chem. Inf. Model., January, 2024
2023
Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.
J. Chem. Inf. Model., September, 2023
2022
Optimized Mappings for Symmetric Range-Limited Molecular Force Calculations on FPGAs.
Proceedings of the 32nd International Conference on Field-Programmable Logic and Applications, 2022
2021
Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones.
PLoS Comput. Biol., 2021
Proceedings of the 2021 IEEE High Performance Extreme Computing Conference, 2021
Proceedings of the 29th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2021
2020
Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery.
J. Chem. Inf. Model., 2020
Proceedings of the 2020 IEEE High Performance Extreme Computing Conference, 2020
2019
Proceedings of the International Conference for High Performance Computing, 2019
Proceedings of the 30th IEEE International Conference on Application-specific Systems, 2019
2018
Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces.
J. Chem. Inf. Model., 2018
2017
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
J. Chem. Inf. Model., December, 2017
J. Chem. Inf. Model., June, 2017
2016
Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications.
J. Chem. Inf. Model., 2016
J. Chem. Inf. Model., 2016
J. Chem. Inf. Model., 2016
Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.
J. Comput. Chem., 2016
In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor.
J. Comput. Aided Mol. Des., 2016
2015
J. Chem. Inf. Model., 2015
Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling.
J. Comput. Aided Mol. Des., 2015
2014
A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring.
J. Chem. Inf. Model., 2014
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A<sub>2A</sub> Receptor.
J. Chem. Inf. Model., 2014
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA.
J. Chem. Inf. Model., 2014
Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases.
J. Cheminformatics, 2014
2013
Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking.
J. Chem. Inf. Model., 2013
Structure-Based Virtual Screening of MT<sub>2</sub> Melatonin Receptor: Influence of Template Choice and Structural Refinement.
J. Chem. Inf. Model., 2013
Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization.
J. Chem. Inf. Model., 2013
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments.
J. Comput. Aided Mol. Des., 2013
Erratum to: Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.
J. Comput. Aided Mol. Des., 2013
2012
Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis.
J. Chem. Inf. Model., 2012
Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines.
J. Chem. Inf. Model., 2012
Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.
J. Comput. Aided Mol. Des., 2012
Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors.
J. Comput. Aided Mol. Des., 2012
2011
Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring.
J. Chem. Inf. Model., 2011
Generation of structure-based pharmacophores using energetic analysis - application on fragment docking.
J. Cheminformatics, 2011
Analysis and comparison of 2D fingerprints: insights into database screening performance using eight fingerprint methods.
J. Cheminformatics, 2011
2010
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers.
J. Chem. Inf. Model., 2010
Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments.
J. Chem. Inf. Model., 2010
2009
J. Chem. Inf. Model., 2009
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation.
J. Comput. Aided Mol. Des., 2009
2008
J. Comput. Aided Mol. Des., 2008