datreant: persistent, Pythonic trees for heterogeneous data. - David L. Dotson; Sean L. Seyler; Max Linke; Richard J. Gowers; Oliver Beckstein (SciPy, 2016)

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. - Richard J. Gowers; Max Linke; Jonathan Barnoud; Tyler J. E. Reddy; Manuel N. Melo; Sean L. Seyler; Jan J. Domanski; David L. Dotson; Sébastien Buchoux; Ian M. Kenney; Oliver Beckstein (SciPy, 2016)

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. - Peter K. Eastman; Pavan Kumar Behara; David L. Dotson; Raimondas Galvelis; John E. Herr; Josh T. Horton; Yuezhi Mao; John D. Chodera; Benjamin P. Pritchard; Yuanqing Wang; Gianni De Fabritiis; Thomas E. Markland (CoRR, 2022)

Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field. - Lorenzo D'amore; David F. Hahn; David L. Dotson; Joshua T. Horton; Jamshed Anwar; Ian Craig; Thomas Fox; Alberto Gobbi; Sirish Kaushik Lakkaraju; Xavier Lucas; Katharina Meier; David L. Mobley; et al. (J. Chem. Inf. Model., 2022)

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. - Joshua T. Horton; Simon Boothroyd; Jeffrey Wagner; Joshua A. Mitchell; Trevor Gokey; David L. Dotson; Pavan Kumar Behara; Venkata Krishnan Ramaswamy; Mark Mackey; John D. Chodera; Jamshed Anwar; David L. Mobley; et al. (J. Chem. Inf. Model., 2022)

alchemlyb: the simple alchemistry library. - Zhiyi Wu; David L. Dotson; Irfan Alibay; Bryce K. Allen; Mohammad Soroush Barhaghi; Jérôme Hénin; Thomas T. Joseph; Ian M. Kenney; Hyungro Lee; Haoxi Li; Victoria T. Lim; Shuai Liu; et al. (J. Open Source Softw., 2024)

alchemlyb. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)

alchemlyb: the simple alchemistry library. - David L. Dotson; Ian M. Kenney; Oliver Beckstein; Shuai Liu; Travis Jensen; Bryce K. Allen; Dominik Wille; Victoria T. Lim; Hyungro Lee; Mohammad Soroush Barhaghi; Zhiyi Wu; Wei-Tse Hsu; et al. (Zenodo, 2024)