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Proteins. 2009;77 Suppl 9:18-28. doi: 10.1002/prot.22561.

Evaluation of template-based models in CASP8 with standard measures.

Author information

1
Department of Biochemical Sciences, Sapienza-University of Rome, P. le A. Moro, 5, 00185 Rome, Italy.
2
Genome Center, University of California, Davis, California 95616.
3
Center for Advanced Research in Biotechnology, University of Maryland, Rockville, Maryland 20850.
4
Department of Biochemistry and Molecular Biophysics, Columbia University, Northeast Structural Genomics Consortium (NESG) and New York Consortium on Membrane Proteins (NYCOMPS), Columbia University, New York, New York 10032.
5
Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza-University of Rome, P. le A. Moro, 5, 00185 Rome, Italy.
#
Contributed equally

Abstract

The strategy for evaluating template-based models submitted to CASP has continuously evolved from CASP1 to CASP5, leading to a standard procedure that has been used in all subsequent editions. The established approach includes methods for calculating the quality of each individual model, for assigning scores based on the distribution of the results for each target and for computing the statistical significance of the differences in scores between prediction methods. These data are made available to the assessor of the template-based modeling category, who uses them as a starting point for further evaluations and analyses. This article describes the detailed workflow of the procedure, provides justifications for a number of choices that are customarily made for CASP data evaluation, and reports the results of the analysis of template-based predictions at CASP8.

PMID:
19731382
PMCID:
PMC4589151
DOI:
10.1002/prot.22561
[Indexed for MEDLINE]
Free PMC Article

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