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Proteins. 2016 Sep;84 Suppl 1:20-33. doi: 10.1002/prot.24982. Epub 2016 Jan 27.

CASP 11 target classification.

Author information

1
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050. lkinch@chop.swmed.edu.
2
Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050.
3
Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050.
4
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050.
5
Institute for Cancer Research, 333 Cottman Avenue, Philadelphia, 19111, Pennsylvania Fox Chase Cancer Center.
6
Genome Center, University of California, 451 Health Sciences Drive, Davis, 95616, California.

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.

KEYWORDS:

CASP11; classification; fold space; free modeling; protein structure; sequence homologs; structure analogs; structure prediction; template-based modeling

PMID:
26756794
PMCID:
PMC4940306
DOI:
10.1002/prot.24982
[Indexed for MEDLINE]
Free PMC Article

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