Development and validation of a modular, extensible docking program: DOCK 5. - Demetri Moustakas; P. Therese Lang; Scott C.-H. Pegg; Eric Pettersen; Irwin D. Kuntz; Natasja Brooijmans; Robert C. Rizzo (J. Comput. Aided Mol. Des., 2006)

Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. - Sudipto Mukherjee 002; Trent E. Balius; Robert C. Rizzo (J. Chem. Inf. Model., 2010)

Implementation and evaluation of a docking-rescoring method using molecular footprint comparisons. - Trent E. Balius; Sudipto Mukherjee 002; Robert C. Rizzo (J. Comput. Chem., 2011)

Evaluation of DOCK 6 as a pose generation and database enrichment tool. - Scott R. Brozell; Sudipto Mukherjee 002; Trent E. Balius; Daniel R. Roe; David A. Case; Robert C. Rizzo (J. Comput. Aided Mol. Des., 2012)

Grid-based molecular footprint comparison method for docking and de novo design: Application to HIVgp41. - Trent E. Balius; William J. Allen; Sudipto Mukherjee 002; Robert C. Rizzo (J. Comput. Chem., 2013)

Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design. - William J. Allen; Robert C. Rizzo (J. Chem. Inf. Model., 2014)

DOCK 6: Impact of new features and current docking performance. - William J. Allen; Trent E. Balius; Sudipto Mukherjee 002; Scott R. Brozell; Demetri Moustakas; P. Therese Lang; David A. Case; Irwin D. Kuntz; Robert C. Rizzo (J. Comput. Chem., 2015)

Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. - William J. Allen; Brian C. Fochtman; Trent E. Balius; Robert C. Rizzo (J. Comput. Chem., 2017)

A molecular evolution algorithm for ligand design in DOCK. - Lauren E. Prentis; Courtney D. Singleton; John D. Bickel; William J. Allen; Robert C. Rizzo (J. Comput. Chem., 2022)

Descriptor-Driven de Novo Design Algorithms for DOCK6 Using RDKit. - Guilherme Duarte Ramos Matos; Steven Pak; Robert C. Rizzo (J. Chem. Inf. Model., 2023)

Fragment and torsion biasing algorithms for construction of small organic molecules in proteins using DOCK. - John D. Bickel; Brock T. Boysan; Robert C. Rizzo (J. Comput. Chem., 2025)

Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set. - Y. Stanley Tan; Mayukh Chakrabarti; Reed M. Stein; Lauren E. Prentis; Robert C. Rizzo; Tom Kurtzman; Marcus Fischer; Trent E. Balius (J. Chem. Inf. Model., 2025)