Lemon: a framework for rapidly mining structural information from the Protein Data Bank. - Jonathan Fine; Gaurav Chopra (Bioinform., 2019)

CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. - Jonathan Fine; Janez Konc; Ram Samudrala; Gaurav Chopra (J. Chem. Inf. Model., 2020)

DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening. - Jonathan Fine; Matthew Muhoberac; Guillaume Fraux; Gaurav Chopra (J. Chem. Inf. Model., 2020)

Dedenser: A Python Package for Clustering and Downsampling Chemical Libraries. - Armen G. Beck; Jonathan Fine; Yu-hong Lam; Edward C. Sherer; Erik L. Regalado; Pankaj Aggarwal (J. Chem. Inf. Model., 2025)