ArticleJournal of biomolecular NMR2012
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Article in Journal of biomolecular NMR, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Structure and Gating Behavior of the Human Integral Membrane Protein VDAC1 in a Lipid Bilayer.Journal of the American Chemical Society · 2022Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- A method for validating the accuracy of NMR protein structures.Nature communications · 2020Article
- A pan-cancer assessment of alterations of the kinase domain of ULK1, an upstream regulator of autophagy.Scientific reports · 2020Article
- Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2.Scientific reports · 2019Article
- 2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content.Nucleic acids research · 2019Article
- Effect of low complexity regions within the PvMSP3α block II on the tertiary structure of the protein and implications to immune escape mechanisms.BMC structural biology · 2019Article
- Mollib: a molecular and NMR data analysis software.Journal of biomolecular NMR · 2017Article
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Frontiers in plant science · 2017Article
- Insights from the protein-protein interaction network analysis of Mycobacterium tuberculosis toxin-antitoxin systems.Bioinformation · 2017Article
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- Resolution ofIUCrJ · 2016Article
- Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.Journal of molecular biology · 2016Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating "equivalent resolution" from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 Å) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure "Resolution-by-Proxy" or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect. The ResProx web server is available at http://www.resprox.ca.
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