Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps

Handle URI:
http://hdl.handle.net/10754/559102
Title:
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps
Authors:
Oliva, Romina; Chermak, Edrisse ( 0000-0002-2716-5724 ) ; Cavallo, Luigi ( 0000-0002-1398-338X )
Abstract:
In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.
KAUST Department:
KAUST Catalysis Center (KCC); Physical Sciences and Engineering (PSE) Division
Citation:
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps 2015, 20 (7):12045 Molecules
Publisher:
MDPI AG
Journal:
Molecules
Issue Date:
1-Jul-2015
DOI:
10.3390/molecules200712045
Type:
Article
ISSN:
1420-3049
Additional Links:
http://www.mdpi.com/1420-3049/20/7/12045/
Appears in Collections:
Articles; Physical Sciences and Engineering (PSE) Division; KAUST Catalysis Center (KCC)

Full metadata record

DC FieldValue Language
dc.contributor.authorOliva, Rominaen
dc.contributor.authorChermak, Edrisseen
dc.contributor.authorCavallo, Luigien
dc.date.accessioned2015-07-07T07:35:17Zen
dc.date.available2015-07-07T07:35:17Zen
dc.date.issued2015-07-01en
dc.identifier.citationAnalysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps 2015, 20 (7):12045 Moleculesen
dc.identifier.issn1420-3049en
dc.identifier.doi10.3390/molecules200712045en
dc.identifier.urihttp://hdl.handle.net/10754/559102en
dc.description.abstractIn view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions.en
dc.publisherMDPI AGen
dc.relation.urlhttp://www.mdpi.com/1420-3049/20/7/12045/en
dc.rightsThis is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0/en
dc.subjectrankingen
dc.subjectscoringen
dc.subjectanalysisen
dc.subjectdocking decoysen
dc.subjectdocking modelsen
dc.subjectconsensusen
dc.subjectcontact mapsen
dc.subjectinter-molecular contactsen
dc.subjectprotein-protein interactionsen
dc.subjectstructure predictionen
dc.subjectinterfaceen
dc.subjectCOCOMAPSen
dc.subjectCONSRANKen
dc.subjectCAPRIen
dc.titleAnalysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Mapsen
dc.typeArticleen
dc.contributor.departmentKAUST Catalysis Center (KCC)en
dc.contributor.departmentPhysical Sciences and Engineering (PSE) Divisionen
dc.identifier.journalMoleculesen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDepartment of Sciences and Technologies, University "Parthenope" of Naples, Centro Direzionale Isola C4, 80143 Naples, Italyen
kaust.authorChermak, Edrisseen
kaust.authorCavallo, Luigien
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