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Database (2009) Vol. 2009:bap003; doi:10.1093/database/bap003 published on April 28, 2009
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© 2009 The Author(s).
This is Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Analysis of CASP8 targets, predictions and assessment methods

ShuoYong Shi1, Jimin Pei1, Ruslan I. Sadreyev1, Lisa N. Kinch1, Indraneel Majumdar2, Jing Tong2, Hua Cheng1, Bong-Hyun Kim2 and Nick V. Grishin1,2,*

1Howard Hughes Medical Institute and 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA

*Corresponding author: Tel: 214-645-5946; Fax: 214-645-5948; Email: grishin{at}chop.swmed.edu


  Abstract

Results of the recent Critical Assessment of Techniques for Protein Structure Prediction, CASP8, present several valuable sources of information. First, CASP targets comprise a realistic sample of currently solved protein structures and exemplify the corresponding challenges for predictors. Second, the plethora of predictions by all possible methods provides an unusually rich material for evolutionary analysis of target proteins. Third, CASP results show the current state of the field and highlight specific problems in both predicting and assessing. Finally, these data can serve as grounds to develop and analyze methods for assessing prediction quality. Here we present results of our analysis in these areas. Our objective is not to duplicate CASP assessment, but to use our unique experience as former CASP5 assessors and CASP8 predictors to (i) offer more insights into CASP targets and predictions based on expert analysis, including invaluable analysis prior to target structure release; and (ii) develop an assessment methodology tailored towards current challenges in the field. Specifically, we discuss preparing target structures for assessment, parsing protein domains, balancing evaluations based on domains and on whole chains, dividing targets into categories and developing new evaluation scores. We also present evolutionary analysis of the most interesting and challenging targets.

Database URL: Our results are available as a comprehensive database of targets and predictions at http://prodata.swmed.edu/CASP8.

Received January 27, 2009; Accepted February 21, 2009


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