ArticleProteins2016
Molprobity's ultimate rotamer-library distributions for model validation.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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70 citing papers in PubMed.
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- Intrinsic conformational equilibria position arrestin-2 for activation.bioRxiv : the preprint server for biology · 2025Article
- AQuaRef: machine learning accelerated quantum refinement of protein structures.Nature communications · 2025Article
- Computational design of an mRNA vaccine targeting antifungal-resistant Lomentospora prolificans.Scientific reports · 2025Article
- Computational Evidence for Digenic Contribution ofInternational journal of molecular sciences · 2025Article
- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
- Cis-nonProline peptides: Genuine occurrences and their functional roles.Protein science : a publication of the Protein Society · 2025Article
- PhiSiCal-Checkup: A Bayesian framework to validate amino acid conformations within experimental protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structure-driven development of a biomimetic rare earth artificial metalloprotein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Protonation of histidine rings using quantum-mechanical methods.Acta crystallographica. Section D, Structural biology · 2024Article
- AutoEpiCollect, a Novel Machine Learning-Based GUI Software for Vaccine Design: Application to Pan-Cancer Vaccine Design Targeting PIK3CA Neoantigens.Bioengineering (Basel, Switzerland) · 2024Article
- DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting.Briefings in bioinformatics · 2024Article
- Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP.Communications biology · 2024Article
- ATLAS: protein flexibility description from atomistic molecular dynamics simulations.Nucleic acids research · 2024Article
- One bead per residue can describe all-atom protein structures.Structure (London, England : 1993) · 2024Article
10 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-specific filters for electron-density value and model-to-density fit. The combined new protocol retains a million residues of data, while cleaning up false-positive noise in the multi- χ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000-fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond-angle deviations in enabling presumably strained side-chain conformations. Further, along with favored and outlier, an allowed category (0.3-2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model-building and refinement. The multi-dimensional χ distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed "ultimate" because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side-chain with backbone criteria. Proteins 2016; 84:1177-1189. © 2016 Wiley Periodicals, Inc.
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