Diversity Profiling and Design Using 3D Pharmacophores: Pharmacophore-Derived Queries (PDQ). - Stephen D. Pickett; Jonathan S. Mason; Iain M. McLay (J. Chem. Inf. Comput. Sci., 1996)

Similarity Measures for Rational Set Selection and Analysis of Combinatorial Libraries: The Diverse Property-Derived (DPD) Approach. - Richard A. Lewis; Jonathan S. Mason; Iain M. McLay (J. Chem. Inf. Comput. Sci., 1997)

Rational Screening Set Design and Compound Selection: Cascaded Clustering. - Paul R. Menard; Richard A. Lewis; Jonathan S. Mason (J. Chem. Inf. Comput. Sci., 1998)

Chemistry Space Metrics in Diversity Analysis, Library Design, and Compound Selection. - Paul R. Menard; Jonathan S. Mason; Isabelle Morize; Susanne Bauerschmidt (J. Chem. Inf. Comput. Sci., 1998)

Ligand-Receptor 3-D Similarity Studies Using Multiple 4-Point Pharmacophores. - Jonathan S. Mason; Daniel L. Cheney (Pacific Symposium on Biocomputing, 1999)

Descriptors you can count on? Normalized and filtered pharmacophore descriptors for virtual screening. - Andrew C. Good; Sung-Jin Cho; Jonathan S. Mason (J. Comput. Aided Mol. Des., 2004)

A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP): Theory and Application. - Massimo Baroni; Gabriele Cruciani; Simone Sciabola; Francesca Perruccio; Jonathan S. Mason (J. Chem. Inf. Model., 2007)

Designing Compound Subsets: Comparison of Random and Rational Approaches Using Statistical Simulation. - Siew K. Yeap; Rosalind J. Walley; Michael Snarey; Willem P. van Hoorn; Jonathan S. Mason (J. Chem. Inf. Model., 2007)

High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields. - Simone Sciabola; Robert V. Stanton; James E. J. Mills; Maria M. Flocco; Massimo Baroni; Gabriele Cruciani; Francesca Perruccio; Jonathan S. Mason (J. Chem. Inf. Model., 2010)

Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. - Andrea Bortolato; Benjamin G. Tehan; Michael S. Bodnarchuk; Jonathan W. Essex; Jonathan S. Mason (J. Chem. Inf. Model., 2013)

Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case. - Andrea Bortolato; Francesca Deflorian; Dahlia R. Weiss; Jonathan S. Mason (J. Chem. Inf. Model., 2015)

GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking. - Dahlia R. Weiss; Andrea Bortolato; Benjamin G. Tehan; Jonathan S. Mason (J. Chem. Inf. Model., 2016)

Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. - Giulio Mattedi; Francesca Deflorian; Jonathan S. Mason; Chris de Graaf; Francesco L. Gervasio (J. Chem. Inf. Model., 2019)

Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. - Francesca Deflorian; Laura Pérez-Benito; Eelke B. Lenselink; Miles Congreve; Herman W. T. van Vlijmen; Jonathan S. Mason; Chris de Graaf; Gary Tresadern (J. Chem. Inf. Model., 2020)