ArticleJournal of structural and functional genomics2005
A test of enhancing model accuracy in high-throughput crystallography.
Article in Journal of structural and functional genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
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- Potential therapeutic target identification in the novel 2019 coronavirus: insight from homology modeling and blind docking study.The Egyptian journal of medical human genetics · 2020Article
- Model validation: local diagnosis, correction and when to quit.Acta crystallographica. Section D, Structural biology · 2018Article
- Tetrahydrocarbazoles are a novel class of potent P-type ATPase inhibitors with antifungal activity.PloS one · 2018Article
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- Recommendations of the wwPDB NMR Validation Task Force.Structure (London, England : 1993) · 2013Article
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- Studying and polishing the PDB's macromolecules.Biopolymers · 2013Review
- Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.Annual review of biophysics · 2013Review
- Doing molecular biophysics: finding, naming, and picturing signal within complexity.Annual review of biophysics · 2013Article
- A new generation of crystallographic validation tools for the protein data bank.Structure (London, England : 1993) · 2011Article
- The Phenix software for automated determination of macromolecular structures.Methods (San Diego, Calif.) · 2011Article
- Alternate states of proteins revealed by detailed energy landscape mapping.Journal of molecular biology · 2011Article
- PHENIX: a comprehensive Python-based system for macromolecular structure solution.Acta crystallographica. Section D, Biological crystallography · 2010Article
- MolProbity: all-atom structure validation for macromolecular crystallography.Acta crystallographica. Section D, Biological crystallography · 2010Article
- The distal pocket histidine residue in horse heart myoglobin directs the O-binding mode of nitrite to the heme iron.Journal of the American Chemical Society · 2009Article
- KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program.Protein science : a publication of the Protein Society · 2009Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The high throughput of structure determination pipelines relies on increased automation and, consequently, a reduction of time spent on interactive quality control. In order to meet and exceed current standards in model accuracy, new approaches are needed for the facile identification and correction of model errors during refinement. One such approach is provided by the validation and structure-improvement tools of the MOL: PROBITY: web service. To test their effectiveness in high-throughput mode, a large subset of the crystal structures from the SouthEast Collaboratory for Structural Genomics (SECSG) has used protocols based on the MOL: PROBITY: tools. Comparison of 29 working-set and 19 control-set SECSG structures shows that working-set outlier scores for updated Ramachandran-plot, sidechain rotamer, and all-atom steric criteria have been improved by factors of 5- to 10-fold (relative to the control set or to a Protein Data Bank sample), while quality of covalent geometry, R(work), R(free), electron density and difference density are maintained or improved. Some parts of this correction process are already fully automated; other parts involve manual rebuilding of conformations flagged by the tests as trapped in the wrong local minimum, often altering features of functional significance. The ease and effectiveness of this technique shows that macromolecular crystal structures from either traditional or high-throughput determinations can feasibly reach a new level of excellence in conformational accuracy and reliability.
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Registered trials
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