Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

Handle URI:
http://hdl.handle.net/10754/563043
Title:
Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models
Authors:
Vangone, Anna; Cavallo, Luigi ( 0000-0002-1398-338X ) ; Oliva, Romina M.
Abstract:
Herein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most frequently observed contacts. We applied CONSRANK to 19 CAPRI protein-protein targets, covering a wide range of prediction difficulty and involved in a variety of biological functions. CONSRANK results are consistently good, both in terms of native-like (NL) solutions ranked in the top positions and of values of the Area Under the receiver operating characteristic Curve (AUC). For targets having a percentage of NL solutions above 3%, an excellent performance is found, with AUC values approaching 1. For the difficult target T46, having only 3.4% NL solutions, the number of NL solutions in the top 5 and 10 ranked positions is enriched by a factor 30, and the AUC value is as high as 0.997. AUC values below 0.8 are only found for targets featuring a percentage of NL solutions within 1.1%. Remarkably, a false consensus emerges only in one case, T42, which happens to be an artificial protein, whose assembly details remain uncertain, based on controversial experimental data. We also show that CONSRANK still performs very well on a limited number of models, provided that more than 1 NL solution is included in the ensemble, thus extending its applicability to cases where few dozens of models are available.© 2013 Wiley Periodicals, Inc.
KAUST Department:
KAUST Catalysis Center (KCC); Physical Sciences and Engineering (PSE) Division; Chemical Science Program
Publisher:
Wiley-Blackwell
Journal:
Proteins: Structure, Function, and Bioinformatics
Issue Date:
17-Oct-2013
DOI:
10.1002/prot.24423
PubMed ID:
24115176
Type:
Article
ISSN:
08873585
Appears in Collections:
Articles; Physical Sciences and Engineering (PSE) Division; Chemical Science Program; KAUST Catalysis Center (KCC)

Full metadata record

DC FieldValue Language
dc.contributor.authorVangone, Annaen
dc.contributor.authorCavallo, Luigien
dc.contributor.authorOliva, Romina M.en
dc.date.accessioned2015-08-03T11:34:27Zen
dc.date.available2015-08-03T11:34:27Zen
dc.date.issued2013-10-17en
dc.identifier.issn08873585en
dc.identifier.pmid24115176en
dc.identifier.doi10.1002/prot.24423en
dc.identifier.urihttp://hdl.handle.net/10754/563043en
dc.description.abstractHerein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most frequently observed contacts. We applied CONSRANK to 19 CAPRI protein-protein targets, covering a wide range of prediction difficulty and involved in a variety of biological functions. CONSRANK results are consistently good, both in terms of native-like (NL) solutions ranked in the top positions and of values of the Area Under the receiver operating characteristic Curve (AUC). For targets having a percentage of NL solutions above 3%, an excellent performance is found, with AUC values approaching 1. For the difficult target T46, having only 3.4% NL solutions, the number of NL solutions in the top 5 and 10 ranked positions is enriched by a factor 30, and the AUC value is as high as 0.997. AUC values below 0.8 are only found for targets featuring a percentage of NL solutions within 1.1%. Remarkably, a false consensus emerges only in one case, T42, which happens to be an artificial protein, whose assembly details remain uncertain, based on controversial experimental data. We also show that CONSRANK still performs very well on a limited number of models, provided that more than 1 NL solution is included in the ensemble, thus extending its applicability to cases where few dozens of models are available.© 2013 Wiley Periodicals, Inc.en
dc.publisherWiley-Blackwellen
dc.subjectCAPRIen
dc.subjectCONS-COCOMAPSen
dc.subjectConsensusen
dc.subjectCONSRANKen
dc.subjectDocking modelsen
dc.subjectInter-molecular contactsen
dc.subjectProtein-protein interactionsen
dc.subjectRankingen
dc.subjectScoringen
dc.titleUsing a consensus approach based on the conservation of inter-residue contacts to rank CAPRI modelsen
dc.typeArticleen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.contributor.departmentChemical Science Programen
dc.identifier.journalProteins: Structure, Function, and Bioinformaticsen
dc.contributor.institutionDepartment of Chemistry and Biology, University of Salerno, Via ponte don Melillo, Fisciano (SA), 84084, Italyen
dc.contributor.institutionDepartment of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4 80143, Naples, Italyen
kaust.authorCavallo, Luigien

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