Xenolog classification. - Charlotte A. Darby; Maureen Stolzer; Patrick J. Ropp; Daniel Barker; Dannie Durand (Bioinform., 2017)

Scoria: a Python module for manipulating 3D molecular data. - Patrick J. Ropp; Aaron J. Friedman; Jacob D. Durrant (J. Cheminformatics, 2017)

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)

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening. - Patrick J. Ropp; Jacob O. Spiegel; Jennifer L. Walker; Harrison Green; Guillermo A. Morales; Katherine A. Milliken; John J. Ringe; Jacob D. Durrant (J. Cheminformatics, 2019)