ESCHER-A Computer Program for the Determination of External Rotational Symmetry Numbers from Molecular Topology. - W. Patrick Walters; Samuel H. Yalkowsky (J. Chem. Inf. Comput. Sci., 1996)

Filtering databases and chemical libraries. - Paul S. Charifson; W. Patrick Walters (J. Comput. Aided Mol. Des., 2002)

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. - Imran S. Haque; Vijay S. Pande; W. Patrick Walters (J. Chem. Inf. Model., 2010)

Anatomy of High-Performance 2D Similarity Calculations. - Imran S. Haque; Vijay S. Pande; W. Patrick Walters (J. Chem. Inf. Model., 2011)

Alpha shock. - Mark A. Murcko; W. Patrick Walters (J. Comput. Aided Mol. Des., 2012)

Modeling, Informatics, and the Quest for Reproducibility. - W. Patrick Walters (J. Chem. Inf. Model., 2013)

Understanding covariate shift in model performance. - Georgia B. McGaughey; W. Patrick Walters; Brian Goldman (F1000Research, 2016)

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. - Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A. Stuckey; You-Na Kang; Jim Delproposto; Ginger Kubish; James B. Dunbar Jr.; Heather A. Carlson; Stephen K. Burley; W. Patrick Walters; et al. (J. Comput. Aided Mol. Des., 2016)

Prediction of Protein Pairs Sharing Common Active Ligands Using Protein Sequence, Structure, and Ligand Similarity. - Yu-Chen Chen; Robert Tolbert; Alex M. Aronov; Georgia B. McGaughey; W. Patrick Walters; Lidio Meireles (J. Chem. Inf. Model., 2016)

Modeling & Informatics at Vertex Pharmaceuticals Incorporated: our philosophy for sustained impact. - Georgia B. McGaughey; W. Patrick Walters (J. Comput. Aided Mol. Des., 2017)

D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Zied Gaieb; Shuai Liu; Symon Gathiaka; Michael Chiu; Huanwang Yang; Chenghua Shao; Victoria A. Feher; W. Patrick Walters; Bernd Kuhn; Markus G. Rudolph; Stephen K. Burley; Michael K. Gilson; et al. (J. Comput. Aided Mol. Des., 2018)

D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. - Zied Gaieb; Conor D. Parks; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Millard H. Lambert; Neysa Nevins; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; Stephen K. Burley; et al. (J. Comput. Aided Mol. Des., 2019)

New Trends in Virtual Screening. - W. Patrick Walters; Renxiao Wang (J. Chem. Inf. Model., 2019)

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. - Conor D. Parks; Zied Gaieb; Michael Chiu; Huanwang Yang; Chenghua Shao; W. Patrick Walters; Johanna M. Jansen; Georgia B. McGaughey; Richard A. Lewis; Scott D. Bembenek; Michael K. Ameriks; Tara Mirzadegan; et al. (J. Comput. Aided Mol. Des., 2020)

Code Sharing in the Open Science Era. - W. Patrick Walters (J. Chem. Inf. Model., 2020)

Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator. - Veerabahu Shanmugasundaram; Jürgen Bajorath; Ralph E. Christoffersen; James D. Petke; W. Jeffrey Howe; Mark A. Johnson; Dimitris K. Agrafiotis; Pil Lee; Leslie A. Kuhn; Jay T. Goodwin; M. Katharine Holloway; Thompson N. Doman; et al. (J. Comput. Aided Mol. Des., 2022)

Comparing classification models - a practical tutorial. - W. Patrick Walters (J. Comput. Aided Mol. Des., 2022)

Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows. - Ajay N. Jain; Ann E. Cleves; W. Patrick Walters (CoRR, 2024)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

A call for an industry-led initiative to critically assess machine learning for real-world drug discovery. - Cas Wognum; Jeremy R. Ash; Matteo Aldeghi; Raquel Rodríguez-Pérez; Cheng Fang; Alan C. Cheng; Daniel J. Price; Djork-Arné Clevert; Ola Engkvist; W. Patrick Walters (Nat. Mac. Intell., 2024)

Thompson Sampling─An Efficient Method for Searching Ultralarge Synthesis on Demand Databases. - Kathryn Klarich; Brian Goldman; Trevor Kramer; Patrick Riley; W. Patrick Walters (J. Chem. Inf. Model., 2024)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. - Christian Kramer; John D. Chodera; Kelly L. Damm-Ganamet; Michael K. Gilson; Judith Guenther; Uta F. Lessel; Richard A. Lewis; David L. Mobley; Eva Nittinger; Adam Pecina; Matthieu Schapira; W. Patrick Walters (J. Chem. Inf. Model., 2025)