A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. - Thijs Beuming; Harel Weinstein (Bioinform., 2004)

PDZBase: a protein?Cprotein interaction database for PDZ-domains. - Thijs Beuming; Lucy Skrabanek; Masha Y. Niv; Piali Mukherjee; Harel Weinstein (Bioinform., 2005)

TRAC: A Platform for Structure-Function Studies of NSS-Proteins Integrates Information from Bioinformatics and Biomedical Literature. - Lei Shi 006; Marko Srdanovic; Thijs Beuming; Lucy Skrabanek; Jonathan A. Javitch; Harel Weinstein (BIBE, 2010)

Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines. - Thijs Beuming; Woody Sherman (J. Chem. Inf. Model., 2012)

Structure-Based Virtual Screening of MT2 Melatonin Receptor: Influence of Template Choice and Structural Refinement. - Daniele Pala; Thijs Beuming; Woody Sherman; Alessio Lodola; Silvia Rivara; Marco Mor (J. Chem. Inf. Model., 2013)

Improved Docking of Polypeptides with Glide. - Ivan Tubert-Brohman; Woody Sherman; Matthew P. Repasky; Thijs Beuming (J. Chem. Inf. Model., 2013)

Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor. - Eelke B. Lenselink; Thijs Beuming; Woody Sherman; Herman W. T. van Vlijmen; Adriaan P. IJzerman (J. Chem. Inf. Model., 2014)

Predicting GPCR Promiscuity Using Binding Site Features. - Anat Levit; Thijs Beuming; Goran Krilov; Woody Sherman; Masha Y. Niv (J. Chem. Inf. Model., 2014)

In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. - Eelke B. Lenselink; Thijs Beuming; Corine van Veen; Arnault Massink; Woody Sherman; Herman W. T. van Vlijmen; Adriaan P. IJzerman (J. Comput. Aided Mol. Des., 2016)

Relative Binding Free Energy Calculations Applied to Protein Homology Models. - Daniel Cappel; Michelle Lynn Hall; Eelke B. Lenselink; Thijs Beuming; Jun Qi; James Bradner; Woody Sherman (J. Chem. Inf. Model., 2016)

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. - Phani Ghanakota; Herman van Vlijmen; Woody Sherman; Thijs Beuming (J. Chem. Inf. Model., 2018)

Rigorous Free Energy Simulations in Virtual Screening. - Zoe Cournia; Bryce K. Allen; Thijs Beuming; David A. Pearlman; Brian K. Radak; Woody Sherman (J. Chem. Inf. Model., 2020)

Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures. - Thijs Beuming; Helena Martín; Anna M. Díaz-Rovira; Lucía Díaz; Victor Guallar; Soumya S. Ray (J. Chem. Inf. Model., 2022)

Are Deep Learning Structural Models Sufficiently Accurate for Virtual Screening? Application of Docking Algorithms to AlphaFold2 Predicted Structures. - Anna M. Díaz-Rovira; Helena Martín; Thijs Beuming; Lucía Díaz; Victor Guallar; Soumya S. Ray (J. Chem. Inf. Model., 2023)