Journal article
Assessment of the protein-structure refinement category in CASP8
Proteins, structure, function, and bioinformatics, Vol.77(Suppl 9), pp.66-80
2009
DOI: 10.1002/prot.22538
PMCID: PMC2801025
PMID: 19714776
Abstract
Here, we summarize the assessment of protein structure refinement in CASP8. Twenty-four groups refined a total of twelve target proteins. Averaging over all groups and all proteins, there was no net improvement over the original starting models. However, there are now some individual research groups who consistently do improve protein structures relative to a starting starting model. We compare various measures of quality assessment, including (i) standard backbone-based methods, (ii) new methods from the Richardson group, and (iii) ensemble-based methods for comparing experimental structures, such as NMR NOE violations and the suitability of the predicted models to serve as templates for molecular replacement. On the whole, there is a general correlation among various measures. However, there are interesting differences. Sometimes a structure that is in better agreement with the experimental data is judged to be slightly worse by GDT-TS. This suggests that for comparing protein structures that are already quite close to the native, it may be preferable to use ensemble-based experimentally derived measures of quality, in addition to single-structure-based methods such as GDT-TS.
Details
- Title: Subtitle
- Assessment of the protein-structure refinement category in CASP8
- Creators
- Justin L MacCallum - Department of Pharmaceutical Chemistry, University of California San FranciscoLan Hua - Department of Pharmaceutical Chemistry, University of California San FranciscoMichael J Schnieders - Department of Chemistry, Stanford UniversityVijay S Pande - Department of Chemistry, Stanford UniversityMatthew P Jacobson - Department of Pharmaceutical Chemistry, University of California San FranciscoKen A Dill - Department of Pharmaceutical Chemistry, University of California San Francisco
- Resource Type
- Journal article
- Publication Details
- Proteins, structure, function, and bioinformatics, Vol.77(Suppl 9), pp.66-80
- DOI
- 10.1002/prot.22538
- PMID
- 19714776
- PMCID
- PMC2801025
- ISSN
- 0887-3585
- eISSN
- 1097-0134
- Language
- English
- Date published
- 2009
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Biochemistry and Molecular Biology
- Record Identifier
- 9984024551002771
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