GNINA 1.0: molecular docking with deep learning. - Andrew T. McNutt; Paul G. Francoeur; Rishal Aggarwal; Tomohide Masuda; Rocco Meli; Matthew Ragoza; Jocelyn Sunseri; David Ryan Koes (J. Cheminformatics, 2021)

Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. - Andrew T. McNutt; David Ryan Koes (J. Chem. Inf. Model., 2022)

Conformer Generation for Structure-Based Drug Design: How Many and How Good? - Andrew T. McNutt; Fatimah Bisiriyu; Sophia Song; Ananya Vyas; Geoffrey R. Hutchison; David Ryan Koes (J. Chem. Inf. Model., 2023)

SPRINT Enables Interpretable and Ultra-Fast Virtual Screening against Thousands of Proteomes. - Andrew T. McNutt; Abhinav Adduri; Caleb N. Ellington; Monica T. Dayao; Eric P. Xing; Hosein Mohimani; David Ryan Koes (CoRR, 2024)

Open-ComBind: harnessing unlabeled data for improved binding pose prediction. - Andrew T. McNutt; David Ryan Koes (J. Comput. Aided Mol. Des., 2024)

GNINA 1.3: the next increment in molecular docking with deep learning. - Andrew T. McNutt; Yanjing Li; Rocco Meli; Rishal Aggarwal; David Ryan Koes (J. Cheminformatics, 2025)