TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD. - Josh Vincent Vermaas; David J. Hardy; John E. Stone; Emad Tajkhorshid; Axel Kohlmeyer (J. Chem. Inf. Model., 2016)

GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. - Scott LeGrand; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Josh Vincent Vermaas; Rupesh Agarwal; Jeff Larkin; Duncan Poole; Diogo Santos-Martins; Leonardo Solis-Vasquez; Andreas Koch 001; Stefano Forli; et al. (BCB, 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)

Supercomputing Pipelines Search for Therapeutics Against COVID-19. - Josh Vincent Vermaas; Ada Sedova; Matthew B. Baker; Swen Boehm; David M. Rogers 001; Jeff Larkin; Jens Glaser; Micholas Dean Smith; Oscar R. Hernandez; Jeremy C. Smith (Comput. Sci. Eng., 2021)

High-throughput virtual laboratory for drug discovery using massive datasets. - Jens Glaser; Josh Vincent Vermaas; David M. Rogers 001; Jeff Larkin; Scott LeGrand; Swen Boehm; Matthew B. Baker; Aaron Scheinberg; Andreas F. Tillack; Mathialakan Thavappiragasam; Ada Sedova; Oscar R. Hernandez (Int. J. High Perform. Comput. Appl., 2021)

Assembly and Analysis of Cell-Scale Membrane Envelopes. - Josh Vincent Vermaas; Christopher G. Mayne; Eric Shinn; Emad Tajkhorshid (J. Chem. Inf. Model., 2022)

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting". - Daipayan Sarkar; Hyungro Lee; John W. Vant; Matteo Turilli; Josh Vincent Vermaas; Shantenu Jha; Abhishek Singharoy (Zenodo, 2023)

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. - Daipayan Sarkar; Hyungro Lee; John W. Vant; Matteo Turilli; Josh Vincent Vermaas; Shantenu Jha; Abhishek Singharoy (J. Chem. Inf. Model., 2023)