Woody Sherman

According to our database1, Woody Sherman authored at least 39 papers between 2008 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
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Links

Online presence:

On csauthors.net:

Bibliography

2021
System-Level Modeling of GPU/FPGA Clusters for Molecular Dynamics Simulations.
Proceedings of the 2021 IEEE High Performance Extreme Computing Conference, 2021

Upgrade of FPGA Range-Limited Molecular Dynamics to Handle Hundreds of Processors.
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

Rigorous Free Energy Simulations in Virtual Screening.
J. Chem. Inf. Model., 2020

A Communication-Efficient Multi-Chip Design for Range-Limited Molecular Dynamics.
Proceedings of the 2020 IEEE High Performance Extreme Computing Conference, 2020

2019
Fully Integrated On-FPGA Molecular Dynamics Simulations.
CoRR, 2019

Fully integrated FPGA molecular dynamics simulations.
Proceedings of the International Conference for High Performance Computing, 2019

Molecular Dynamics Range-Limited Force Evaluation Optimized for FPGAs.
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

2016
Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications.
J. Chem. Inf. Model., 2016

Automated Protocol for Large-Scale Modeling of Gene Expression Data.
J. Chem. Inf. Model., 2016

Relative Binding Free Energy Calculations Applied to Protein Homology Models.
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
Accurate Binding Free Energy Predictions in Fragment Optimization.
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

Predicting GPCR Promiscuity Using Binding Site Features.
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
Improved Docking of Polypeptides with Glide.
J. Chem. Inf. Model., 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
Novel Method for Generating Structure-Based Pharmacophores Using Energetic Analysis.
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
Improving database enrichment through ensemble docking.
J. Comput. Aided Mol. Des., 2008


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