Quality assessment for molecular models
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Revision as of 23:17, 26 June 2008
The molecular models published in the Protein Data Bank for X-ray crystallography vary widely in quality, and rarely they are grossly incorrect[1]. Generally, model quality is indicated by the resolution of the model, the R value, and especially the Free R. Useful information on model quality, including the Ramachandran plots, can be obtained from PDBReports[2]. All-atom contact analysis[3] is a powerful newer method for finding and correcting errors in crystallographic models, made easy and convenient with the MolProbity Server[4].
Generally, crystallographic models are reliable in most details when they have resolutions of 2.0 Å or better, R values of 0.20 or less, and R free values of 0.25 or less. However, new and important structural insights are often provided by models with much lower resolution.
NMR models are generally less reliable than crystallographic models because the method yields less detailed information. For NMR, there are no widely reported global error estimates equivalent to the crystallographic R value and Free R. Unlike with crystallographic results, it is not possible to distinguish reliable from unreliable NMR models from information included in the PDB files.
Laskowski has provided an outstandingly clear and succinct overview of how to assess model quality. For examples of published crystallographic errors, see Laskowski, and Kleywegt, 2000, and Kleywegt and Brünger, 1996. Kleywegt has also provided an excellent on-line tutorial on model validation.
See Also
References and Websites
- ↑ Miller, Greg (2007) A Scientist's Nightmare: Software Problem Leads to Five Retractions. [http://www.sciencemag.org/cgi/content/summary/314/5807/1856 Science 22 December 2006: 314:1856-7. DOI: 10.1126/science.314.5807.1856].
- ↑ PDBREPORT Database
- ↑ Richardson, Jane S. (2003). All-atom contacts: a new approach to structure validation. Chapter 15 in Structural Bioinformatics (2003) edited by Philip E. Bourne and Helge Weissig, Wiley-Liss, 649 pages. Complete contents at structuralbioinformaticsbook.com.
- ↑ MolProbity Server: All-atom contact analysis, flip corrections for Asn, Gln, His, clash analysis, Ramachandran analysis, and more.
