MolProbity: More and better reference data for improved all‐atom structure validation
Open accessAbstract
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open‐source CCTBX portion of the Phenix software system. This improves long‐term maintainability and enhances the thorough integration of MolProbity‐style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk . GitHub serves our open‐source code, reference datasets, and the resulting multi‐dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His “flip” correction is now more idealized, since the post‐refinement step has apparently often been skipped in the past. Two distinct sets of heavy‐atom‐to‐hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron‐cloud‐center positions suitable for X‐ray crystallography and one for nuclear positions. New validations include messages at input about problem‐causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality‐filtered residues in a new reference dataset, the CaBLAM Cα‐CO virtual‐angle analysis of backbone and secondary structure for cryoEM or low‐resolution X‐ray, and flagging of the very rare cis ‐nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all‐atom clashscore.
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The final structures of FGFR2_mb and the FGFR4D3-FGFR2_mb complex were validated with MolProbity.
“The final structures were validated with MolProbity75,76.”
From Design of protein-binding proteins from the target structure alone (2022) · cites this paper as [76]
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- Authors
- Williams, C. J., Headd, J. J., Moriarty, N. W., Prisant, M. G., Videau, L. L., Deis, L. N., Verma, V., Keedy, D. A., Hintze, B. J., Chen, V. B., Jain, S., Lewis, S. M., Arendall, W. B., Snoeyink, J., Adams, P. D., Lovell, S. C., Richardson, J. S., & Richardson, D. C.
- Affiliations
- Duke University (US)
- Lawrence Berkeley National Laboratory (US)
- University of North Carolina at Chapel Hill (US)
- University of Manchester (GB)
- Corresponding author
- Richardson, David C.
- ORCID
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2017-11-27
- Volume
- 27
- Issue
- 1
- Pages
- 293-315
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC5734394
- OpenAlex
- W2765322245
- Cited by
- 4,599
- References
- 66
- Citations by year
- 2026: 673 · 2025: 822 · 2024: 747 · 2023: 667 · 2022: 682 · 2021: 491 · 2020: 348 · 2019: 133 · 2018: 35
- FWCI
- 60.36
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Protein Science (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Funders
- National Institutes of Health (R01‐GM073919, P01‐GM063210, R01‐GM088674, R01‐GM073930)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- MolProbity, PHENIX, reference dataset, van der Waals radii, protein crystallography, cryo-EM structure
- MeSH terms
- Models, Molecular, Programming Languages, Proteins, Databases, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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