Dataset Information
An automatic method for CASP9 free modeling structure prediction assessment.
Ontology highlight
ABSTRACT: Motivation
Manual inspection has been applied to and is well accepted for assessing critical assessment of protein structure prediction (CASP) free modeling (FM) category predictions over the years. Such manual assessment requires expertise and significant time investment, yet has the problems of being subjective and unable to differentiate models of similar quality. It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models.Results
Inspired by our experience in CASP9 FM category assessment, we developed an automatic superimposition independent method named Quality Control Score (QCS) for structure prediction assessment. QCS captures both global and local structural features, with emphasis on global topology. We applied this method to all FM targets from CASP9, and overall the results showed the best agreement with Manual Inspection Scores among automatic prediction assessment methods previously applied in CASPs, such as Global Distance Test Total Score (GDT_TS) and Contact Score (CS). As one of the important components to guide our assessment of CASP9 FM category predictions, this method correlates well with other scoring methods and yet is able to reveal good-quality models that are missed by GDT_TS.Availability
The script for QCS calculation is available at http://prodata.swmed.edu/QCS/.Contact
grishin@chop.swmed.eduSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Cong Q
PROVIDER: S-EPMC3232368 | biostudies-literature | 2011 Dec
REPOSITORIES: biostudies-literature
Publications
An automatic method for CASP9 free modeling structure prediction assessment.
Bioinformatics (Oxford, England) 20111012 24
<h4>Motivation</h4>Manual inspection has been applied to and is well accepted for assessing critical assessment of protein structure prediction (CASP) free modeling (FM) category predictions over the years. Such manual assessment requires expertise and significant time investment, yet has the problems of being subjective and unable to differentiate models of similar quality. It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objec ...[more]