Handle URI:
http://hdl.handle.net/10754/598252
Title:
Evaluation of residue-residue contact prediction in CASP10
Authors:
Monastyrskyy, Bohdan; D'Andrea, Daniel; Fidelis, Krzysztof; Tramontano, Anna; Kryshtafovych, Andriy
Abstract:
We present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.
Citation:
Monastyrskyy B, D’Andrea D, Fidelis K, Tramontano A, Kryshtafovych A (2013) Evaluation of residue-residue contact prediction in CASP10. Proteins: Structure, Function, and Bioinformatics 82: 138–153. Available: http://dx.doi.org/10.1002/prot.24340.
Publisher:
Wiley-Blackwell
Journal:
Proteins: Structure, Function, and Bioinformatics
KAUST Grant Number:
KUK-I1–012-43
Issue Date:
31-Aug-2013
DOI:
10.1002/prot.24340
PubMed ID:
23760879
PubMed Central ID:
PMC3823628
Type:
Article
ISSN:
0887-3585
Sponsors:
Grant sponsor: US National Institute of General Medical Sciences (NIGMS/NIH); Grant number: R01GM100482 (to K.F.); Grant sponsor: KAUST Award; Grant number: KUK-I1–012-43 (to A.T.); Grant sponsor: EMBO.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorMonastyrskyy, Bohdanen
dc.contributor.authorD'Andrea, Danielen
dc.contributor.authorFidelis, Krzysztofen
dc.contributor.authorTramontano, Annaen
dc.contributor.authorKryshtafovych, Andriyen
dc.date.accessioned2016-02-25T13:17:26Zen
dc.date.available2016-02-25T13:17:26Zen
dc.date.issued2013-08-31en
dc.identifier.citationMonastyrskyy B, D’Andrea D, Fidelis K, Tramontano A, Kryshtafovych A (2013) Evaluation of residue-residue contact prediction in CASP10. Proteins: Structure, Function, and Bioinformatics 82: 138–153. Available: http://dx.doi.org/10.1002/prot.24340.en
dc.identifier.issn0887-3585en
dc.identifier.pmid23760879en
dc.identifier.doi10.1002/prot.24340en
dc.identifier.urihttp://hdl.handle.net/10754/598252en
dc.description.abstractWe present the results of the assessment of the intramolecular residue-residue contact predictions from 26 prediction groups participating in the 10th round of the CASP experiment. The most recently developed direct coupling analysis methods did not take part in the experiment likely because they require a very deep sequence alignment not available for any of the 114 CASP10 targets. The performance of contact prediction methods was evaluated with the measures used in previous CASPs (i.e., prediction accuracy and the difference between the distribution of the predicted contacts and that of all pairs of residues in the target protein), as well as new measures, such as the Matthews correlation coefficient, the area under the precision-recall curve and the ranks of the first correctly and incorrectly predicted contact. We also evaluated the ability to detect interdomain contacts and tested whether the difficulty of predicting contacts depends upon the protein length and the depth of the family sequence alignment. The analyses were carried out on the target domains for which structural homologs did not exist or were difficult to identify. The evaluation was performed for all types of contacts (short, medium, and long-range), with emphasis placed on long-range contacts, i.e. those involving residues separated by at least 24 residues along the sequence. The assessment suggests that the best CASP10 contact prediction methods perform at approximately the same level, and comparably to those participating in CASP9.en
dc.description.sponsorshipGrant sponsor: US National Institute of General Medical Sciences (NIGMS/NIH); Grant number: R01GM100482 (to K.F.); Grant sponsor: KAUST Award; Grant number: KUK-I1–012-43 (to A.T.); Grant sponsor: EMBO.en
dc.publisherWiley-Blackwellen
dc.subjectRRen
dc.subjectCaspen
dc.subjectResidue-residue Contact Predictionen
dc.subject.meshProteinsen
dc.subject.meshModels, Statisticalen
dc.subject.meshProtein Conformationen
dc.subject.meshModels, Molecularen
dc.titleEvaluation of residue-residue contact prediction in CASP10en
dc.typeArticleen
dc.identifier.journalProteins: Structure, Function, and Bioinformaticsen
dc.identifier.pmcidPMC3823628en
dc.contributor.institutionGenome Center, University of California, Davis, California, 95616.en
kaust.grant.numberKUK-I1–012-43en

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