Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules. - Patrick J. Ropp; Jesse C. Kaminsky; Sara Yablonski; Jacob D. Durrant (J. Cheminformatics, 2019)

PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser. - Sayuri Pacheco; Jesse C. Kaminsky; Iurii K. Kochnev; Jacob D. Durrant (J. Chem. Inf. Model., 2019)

Unsupervised discovery of the shared and private geometry in multi-view data. - Sai Koukuntla; Joshua B. Julian; Jesse C. Kaminsky; Manuel Schottdorf; David W. Tank; Carlos D. Brody; Adam S. Charles (CoRR, 2024)