article Open Access (bronze) EN 2016-01-12

CASP 11 target classification

Lisa N. Kinch, Wenlin Li, R. Dustin Schaeffer, Roland L. Dunbrack, Bohdan Monastyrskyy, Andriy Kryshtafovych, Nick V. Grishin

Proteins Structure Function and Bioinformatics, Vol. 84, Issue S1, pp. 20–33 (2016)

Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Fox Chase Cancer Center, University of California, Davis

DOI: 10.1002/prot.24982 PMID: 26756794

View Free PDF Publisher Website Google Scholar

Abstract

Protein target structures for the Critical Assessment of Structure Prediction round 11 (CASP11) and CASP ROLL were split into domains and classified into categories suitable for assessment of template-based modeling (TBM) and free modeling (FM) based on their evolutionary relatedness to existing structures classified by the Evolutionary Classification of Protein Domains (ECOD) database. First, target structures were divided into domain-based evaluation units. Target splits were based on the domain organization of available templates as well as the performance of servers on whole targets compared to split target domains. Second, evaluation units were classified into TBM and FM categories using a combination of measures that evaluate prediction quality and template detectability. Generally, target domains with sequence-related templates and good server prediction performance were classified as TBM, whereas targets without sequence-identifiable templates and low server performance were classified as FM. As in previous CASP experiments, the boundaries for classification were blurred due to the presence of significant insertions and deteriorations in the targets with respect to homologous templates, as well as the presence of templates with partial coverage of new folds. The FM category included 45 target domains, which represents an unprecedented number of difficult CASP targets provided for modeling. Proteins 2016; 84(Suppl 1):20-33. © 2016 Wiley Periodicals, Inc.

Topics

Protein Structure and Dynamics 1.00 RNA and protein synthesis mechanisms 1.00 Enzyme Structure and Function 1.00

Field: Biochemistry, Genetics and Molecular Biology · Subfield: Molecular Biology

Keywords

CASP,Template,Computer science,Protein structure prediction,Domain (mathematical analysis),Sequence (biology),Data mining,Artificial intelligence,Protein structure,Programming language

MeSH Terms

AnimalsAnimalsAnimalsBacteriophagesBacteriophagesBacteriophagesComputer GraphicsComputer Graphics

All Available Versions

PDF Landing page — Proteins Structure Function and Bioinformatics publishedVersion
Landing page — PubMed publishedVersion
Landing page — Europe PMC (PubMed Central) submittedVersion
Landing page — PubMed Central submittedVersion
Landing page — eScholarship (California Digital Library) submittedVersion