Ranking multiple docking solutions based on the conservation of inter-residue contacts

Handle URI:
http://hdl.handle.net/10754/562813
Title:
Ranking multiple docking solutions based on the conservation of inter-residue contacts
Authors:
Oliva, Romina M.; Vangone, Anna; Cavallo, Luigi ( 0000-0002-1398-338X )
Abstract:
Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 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-Jun-2013
DOI:
10.1002/prot.24314
PubMed ID:
23609916
Type:
Article
ISSN:
08873585
Sponsors:
Funding: RO has been supported by the Italian MIUR (Ministero dell'Istruzione, dell'Universita e della Ricerca; Grant PRIN2008). RO thanks Dr. Angelo Ciaramella and Dr. Antonino Staiano for helpful discussions.
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.authorOliva, Romina M.en
dc.contributor.authorVangone, Annaen
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2015-08-03T11:11:15Zen
dc.date.available2015-08-03T11:11:15Zen
dc.date.issued2013-06-17en
dc.identifier.issn08873585en
dc.identifier.pmid23609916en
dc.identifier.doi10.1002/prot.24314en
dc.identifier.urihttp://hdl.handle.net/10754/562813en
dc.description.abstractMolecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.en
dc.description.sponsorshipFunding: RO has been supported by the Italian MIUR (Ministero dell'Istruzione, dell'Universita e della Ricerca; Grant PRIN2008). RO thanks Dr. Angelo Ciaramella and Dr. Antonino Staiano for helpful discussions.en
dc.publisherWiley-Blackwellen
dc.subjectCAPRIen
dc.subjectCONS-COCOMAPSen
dc.subjectCOCOMAPSen
dc.subjectConsensusen
dc.subjectDOCKGROUNDen
dc.subjectDocking decoysen
dc.subjectInter-molecular contactsen
dc.subjectProtein-protein interactionsen
dc.subjectRankingen
dc.subjectRosettaDocken
dc.subjectStructure predictionen
dc.titleRanking multiple docking solutions based on the conservation of inter-residue contactsen
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 Applied Sciences, University Parthenope of Naples, Centro Direzionale Isola C4, Naples, 80143, Italyen
dc.contributor.institutionDepartment of Chemistry and Biology, University of Salerno, Via ponte don Melillo, Fisciano, (SA), 84084, Italyen
kaust.authorCavallo, Luigien

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