List of works - Woody Sherman

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

scientific article published on 18 November 2020

Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery

scientific article published on 16 September 2020

Boosting Virtual Screening Enrichments with Data Fusion: Coalescing Hits from Two-Dimensional Fingerprints, Shape, and Docking ⬇️

scientific article published on July 3, 2013

Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation ⬇️

scientific article published on October 6, 2012

Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure–Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis ⬇️

scientific article published on February 28, 2012

Consensus Induced Fit Docking (cIFD): methodology, validation, and application to the discovery of novel Crm1 inhibitors ⬇️

scientific article published on September 30, 2012

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines ⬇️

scientific article published on November 15, 2012

Exploring Protein Flexibility: Incorporating Structural Ensembles From Crystal Structures and Simulation into Virtual Screening Protocols ⬇️

scientific article published on April 23, 2012

Fast Equilibration of Water between Buried Sites and the Bulk by Molecular Dynamics with Parallel Monte Carlo Water Moves on Graphical Processing Units

scientific article published on 11 November 2021

Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering ⬇️

scientific article published on May 23, 2012

Hole filling and library optimization: Application to commercially available fragment libraries ⬇️

scientific article published on March 24, 2012

Improved Docking of Polypeptides with Glide ⬇️

scientific article published on July 10, 2013

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor

scientific article (publication date: October 2016)

Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization ⬇️

scientific article published on August 19, 2013

Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones

scientific article published on 04 November 2021

Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences

scientific article published on 06 December 2021

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments ⬇️

scientific article published on April 12, 2013

Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring ⬇️

scientific article published on September 15, 2011

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

scientific article

Rigorous Free Energy Simulations in Virtual Screening

scientific article published on 16 June 2020

Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor

scientific article published on 3 June 2014

Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization ⬇️

scientific article published on December 16, 2011

List of works by Woody Sherman