HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales. - Demian Riccardi; Jerry M. Parks; Alexander Johs; Jeremy C. Smith (J. Chem. Inf. Model., 2015)

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. - Hyea Hwang; Anthony Hazel; Peng Lian; Jeremy C. Smith; James C. Gumbart; Jerry M. Parks (J. Comput. Chem., 2020)

The AQUA-MER databases and aqueous speciation server: A web resource for multiscale modeling of mercury speciation. - Peng Lian; Luanjing Guo; Deepa Devarajan; Jerry M. Parks; Scott L. Painter; Scott C. Brooks; Jeremy C. Smith (J. Comput. Chem., 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - Atanu Acharya; Rupesh Agarwal; Matthew B. Baker; Jérôme Baudry; Debsindhu Bhowmik; Swen Böhm; Kendall G. Byler; Sam Yen-Chi Chen; Leighton Coates; Connor J. Cooper; Omar Demerdash; Isabella Daidone; et al. (J. Chem. Inf. Model., 2020)

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement. - Russell B. Davidson; Mathialakan Thavappiragasam; T. Chad Effler; Jess Woods; Dwayne A. Elias; Jerry M. Parks; Ada Sedova (BCB, 2021)

OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. - Russell B. Davidson; Jess Woods; T. Chad Effler; Mathialakan Thavappiragasam; Julie C. Mitchell; Jerry M. Parks; Ada Sedova (Bioinform., 2022)

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - Russell B. Davidson; Mark Coletti; Mu Gao; Bryan Piatkowski; Avinash Sreedasyam; Farhan Quadir; David J. Weston; Jeremy Schmutz; Jianlin Cheng; Jeffrey Skolnick; Jerry M. Parks; Ada Sedova (Bioinform., 2023)

HLA-Clus: HLA class I clustering based on 3D structure. - Yue Shen; Jerry M. Parks; Jeremy C. Smith (BMC Bioinform., 2023)

Comparative Analysis of TCR and TCR-pMHC Complex Structure Prediction Tools. - Yudan Shi; Jerry M. Parks; Jeremy C. Smith (J. Chem. Inf. Model., 2025)