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)

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)

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. - Chimno I. Nnadi; Meredith L. Jenkins; Daniel R. Gentile; Leslie A. Bateman; Daniel Zaidman; Trent E. Balius; Daniel K. Nomura; John E. Burke; Kevan M. Shokat; Nir London (J. Chem. Inf. Model., 2018)

Property-Unmatched Decoys in Docking Benchmarks. - Reed M. Stein; Ying Yang; Trent E. Balius; Matt J. O'Meara; Jiankun Lyu; Jennifer Young; Khanh G. Tang; Brian K. Shoichet; John J. Irwin (J. Chem. Inf. Model., 2021)

DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking. - Trent E. Balius; Y. Stanley Tan; Mayukh Chakrabarti (J. Comput. Chem., 2024)

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)