Protein-Ligand Scoring with Convolutional Neural Networks. - Matthew Ragoza; Joshua E. Hochuli; Elisa Idrobo; Jocelyn Sunseri; David Ryan Koes (J. Chem. Inf. Model., 2017)

Visualizing Convolutional Neural Network Protein-Ligand Scoring. - Joshua E. Hochuli; Alec Helbling; Tamar Skaist; Matthew Ragoza; David Ryan Koes (CoRR, 2018)

SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. - Vinicius M. Alves; Stephen J. Capuzzi; Rodolpho C. Braga; Daniel Robert Korn; Joshua E. Hochuli; Kyle H. Bowler; Adam Yasgar; Ganesha Rai; Anton Simeonov; Eugene N. Muratov; Alexey V. Zakharov; Alexander Tropsha (J. Chem. Inf. Model., 2020)

Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. - Kathryn E. Kirchoff; James Wellnitz; Joshua E. Hochuli; Travis Maxfield; Konstantin I. Popov; Shawn M. Gomez; Alexander Tropsha (ECIR (2), 2024)

One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening. - James Wellnitz; Sankalp Jain; Joshua E. Hochuli; Travis Maxfield; Eugene N. Muratov; Alexander Tropsha; Alexey V. Zakharov (J. Cheminformatics, 2025)