Acknowledgements

Dedication, heritage, and the people and software behind MolProbity Next.

For Jane S. Richardson & David C. Richardson

Who taught us that every atom matters, that the beauty of a protein structure is inseparable from its correctness, and that the best tools are built with equal parts rigor and generosity.

Your vision — that crystallographers deserve honest, all-atom feedback delivered with respect for their craft — became MolProbity, and continues to shape every validation we run today.

The Richardson Laboratory

MolProbity is a product of the Richardson Laboratory in the Department of Biochemistry at Duke University. For over four decades, the lab has developed methods and tools for macromolecular structure validation and visualization — from the original kinemage graphics to the all-atom contact analysis that defines MolProbity's approach.

MolProbity Heritage

The original MolProbity web server was created primarily by Ian W. Davis in the early 2000s, bringing all-atom contact analysis and other Richardsons' Lab validations to the structural biology community through an accessible and easy-to-use web interface. For nearly twenty years, it has served the community almost without interruption, thanks to the efforts of many Richardsons' Lab alumni — especially Christopher Williams and Michael Prisant. With Jane's impending retirement, however, the future of the service is in question. The core code underlying the current version of MolProbity has been largely untouched since it was originally written, and is in need of updating.

MolProbity Next is a ground-up reimagining of the service, built on modern web technologies while preserving the feel and the validation philosophy of the original. It integrates the CCTBX/Phenix validation libraries with interactive 3D visualization and new tools for structural education.

I have endeavoured to incorporate as many of the features and validations of the original MolProbity as possible. I must acknowledge that many of the features in MolProbity Next would have been impossible without the assistance of AI (largely Claude Code, with some initial work by Google Gemini); Claude Code has made it possible to bring features and tools to MolProbity that I had only ever dreamed about, and has brought to life the possibility for MolProbity Next to surpass its predecessor. It is my sincere hope that MolProbity Next will carry on the legacy of MolProbity, and of the Richardsons' Lab.

— Vincent B. Chen

In Memoriam

W. Bryan Arendall III

Bryan was the webmaster and systems administrator for the original MolProbity, the person who kept the server running and accessible to the structural biology community for years. A co-author on many MolProbity publications, his contributions to the project were foundational. He was a proud fan of the University of Kentucky Wildcats, a devoted husband, a lover of science, and a deeply valued member of the Richardson Lab family.

Bryan liked to remind us that he was the ROOT user — master of all things. He wasn’t wrong.

Citing MolProbity

If you use MolProbity in your work, please cite the appropriate paper(s):

Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verber V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB III, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. (2018) MolProbity: More and better reference data for improved all-atom structure validation. Protein Science 27, 293–315.
doi:10.1002/pro.3330

Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D 66, 12–21.
doi:10.1107/S0907444909042073

Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB III, Snoeyink J, Richardson JS, Richardson DC. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research 35, W375–W383.
doi:10.1093/nar/gkm216

Software & Libraries

MolProbity Next is built on an ecosystem of open-source tools and libraries:

CCTBX / Phenix: The Computational Crystallography Toolbox provides the core validation algorithms: Ramachandran analysis, rotamer evaluation, Cβ deviation, clashscore, and more.
BSD-style / cctbx license. cctbx.github.io
Reduce2 & Probe2: Next-generation hydrogen placement and all-atom contact analysis tools, rewritten as part of the CCTBX ecosystem.
Distributed with CCTBX.
Mol* (Molstar): The 3D molecular viewer used for interactive structure visualization on results pages.
MIT license. molstar.org
Moorhen: A web-based molecular graphics application derived from Coot, used for model building and real-space refinement.
LGPL / GPL heritage (from Coot); vendored as a separate bundle. moorhen.org
Django: The Python web framework powering the MolProbity Next server.
BSD 3-Clause license. djangoproject.com

Per-library license texts for the bundled JavaScript viewers are included in the distribution; see the NOTICE file for the full third-party attribution list.

Funding

MolProbity Next development has been supported by grants from the National Institutes of Health and the Phenix Consortium.

License & Source

MolProbity Next is released under the BSD 3-Clause License (Copyright © 2025, Phenix @ LBL). Third-party components retain their own licenses, listed in the NOTICE file that accompanies the source.

See also the Privacy & Data page for how uploaded structures and results are stored and retained.