This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version.
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Comparative Modeling: Assessment
Assessment of predictions submitted for the CASP6 comparative modeling category†
Article first published online: 26 SEP 2005
DOI: 10.1002/prot.20720
Copyright © 2005 Wiley-Liss, Inc.
Issue
Proteins: Structure, Function, and Bioinformatics
Supplement: Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction
Volume 61, Issue Supplement 7, pages 27–45, 2005
Additional Information
How to Cite
Tress, M., Ezkurdia, I., Graña, O., López, G. and Valencia, A. (2005), Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins, 61: 27–45. doi: 10.1002/prot.20720
- †
Publication History
- Issue published online: 29 DEC 2005
- Article first published online: 26 SEP 2005
- Manuscript Accepted: 21 JUN 2005
- Manuscript Received: 31 MAY 2005
- Abstract
- Article
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- Cited By
Keywords:
- target structures;
- structure prediction;
- 3D models;
- side chains;
- rotamers;
- side-chain contacts;
- alignments;
- binding sites;
- refinement
Abstract
Here we present a full overview of the Critical Assessment of Protein Structure Prediction (CASP6) comparative modeling category. Prediction accuracy for the 43 comparative modeling targets was assessed through detailed numerical comparisons between predicted and experimental structures. Assessments using standard measures for model backbone quality and structural alignment accuracy highlighted a small number of groups with stand out predictions and these findings were backed up by statistical comparisons. We were able to carry out evaluations of side-chain contacts predictions and side-chain rotamer accuracy, for which one group turned out to have statistically better predictions. We also assessed the prediction quality of structurally divergent regions and biologically important sites. Interestingly we were able to show that predictors were not predicting these important functional regions with any greater accuracy than the rest of the structure. In addition we investigated the ability of predictors to build models that improve on the structural template and reached some tentative conclusions from comparisons with the previous CASP experiment. Proteins 2005;Suppl 7:27–45. © 2005 Wiley-Liss, Inc.