Critical assessment of methods of protein structure prediction (CASP) - round x

Handle URI:
http://hdl.handle.net/10754/597894
Title:
Critical assessment of methods of protein structure prediction (CASP) - round x
Authors:
Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy; Schwede, Torsten; Tramontano, Anna
Abstract:
This article is an introduction to the special issue of the journal PROTEINS, dedicated to the tenth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. The 10 CASP experiments span almost 20 years of progress in the field of protein structure modeling, and there have been enormous advances in methods and model accuracy in that period. Notable in this round is the first sustained improvement of models with refinement methods, using molecular dynamics. For the first time, we tested the ability of modeling methods to make use of sparse experimental three-dimensional contact information, such as may be obtained from new experimental techniques, with encouraging results. On the other hand, new contact prediction methods, though holding considerable promise, have yet to make an impact in CASP testing. The nature of CASP targets has been changing in recent CASPs, reflecting shifts in experimental structural biology, with more irregular structures, more multi-domain and multi-subunit structures, and less standard versions of known folds. When allowance is made for these factors, we continue to see steady progress in the overall accuracy of models, particularly resulting from improvement of non-template regions.
Citation:
Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A (2013) Critical assessment of methods of protein structure prediction (CASP) - round x. Proteins: Structure, Function, and Bioinformatics 82: 1–6. Available: http://dx.doi.org/10.1002/prot.24452.
Publisher:
Wiley-Blackwell
Journal:
Proteins: Structure, Function, and Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
17-Dec-2013
DOI:
10.1002/prot.24452
PubMed ID:
24344053
PubMed Central ID:
PMC4394854
Type:
Article
ISSN:
0887-3585
Sponsors:
Grant sponsor: the US National Institute of General Medical Sciences (NIGMS/NIH); Grant number: R01GM100482 (to KF); Grant sponsors: KAUST Award KUK-I1-012-43 (to AT) and by EMBO.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMoult, Johnen
dc.contributor.authorFidelis, Krzysztofen
dc.contributor.authorKryshtafovych, Andriyen
dc.contributor.authorSchwede, Torstenen
dc.contributor.authorTramontano, Annaen
dc.date.accessioned2016-02-25T12:58:29Zen
dc.date.available2016-02-25T12:58:29Zen
dc.date.issued2013-12-17en
dc.identifier.citationMoult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A (2013) Critical assessment of methods of protein structure prediction (CASP) - round x. Proteins: Structure, Function, and Bioinformatics 82: 1–6. Available: http://dx.doi.org/10.1002/prot.24452.en
dc.identifier.issn0887-3585en
dc.identifier.pmid24344053en
dc.identifier.doi10.1002/prot.24452en
dc.identifier.urihttp://hdl.handle.net/10754/597894en
dc.description.abstractThis article is an introduction to the special issue of the journal PROTEINS, dedicated to the tenth Critical Assessment of Structure Prediction (CASP) experiment to assess the state of the art in protein structure modeling. The article describes the conduct of the experiment, the categories of prediction included, and outlines the evaluation and assessment procedures. The 10 CASP experiments span almost 20 years of progress in the field of protein structure modeling, and there have been enormous advances in methods and model accuracy in that period. Notable in this round is the first sustained improvement of models with refinement methods, using molecular dynamics. For the first time, we tested the ability of modeling methods to make use of sparse experimental three-dimensional contact information, such as may be obtained from new experimental techniques, with encouraging results. On the other hand, new contact prediction methods, though holding considerable promise, have yet to make an impact in CASP testing. The nature of CASP targets has been changing in recent CASPs, reflecting shifts in experimental structural biology, with more irregular structures, more multi-domain and multi-subunit structures, and less standard versions of known folds. When allowance is made for these factors, we continue to see steady progress in the overall accuracy of models, particularly resulting from improvement of non-template regions.en
dc.description.sponsorshipGrant sponsor: the US National Institute of General Medical Sciences (NIGMS/NIH); Grant number: R01GM100482 (to KF); Grant sponsors: KAUST Award KUK-I1-012-43 (to AT) and by EMBO.en
dc.publisherWiley-Blackwellen
dc.subjectProtein Structure Predictionen
dc.subjectCaspen
dc.subjectCommunity Wide Experimenten
dc.subject.meshProtein Conformationen
dc.subject.meshModels, Molecularen
dc.titleCritical assessment of methods of protein structure prediction (CASP) - round xen
dc.typeArticleen
dc.identifier.journalProteins: Structure, Function, and Bioinformaticsen
dc.identifier.pmcidPMC4394854en
dc.contributor.institutionInstitute for Bioscience and Biotechnology Research and Department of Cell Biology and Molecular Genetics, University of Maryland, Rockville, Maryland, 20850.en
kaust.grant.numberKUK-I1-012-43en

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