Template-based protein–protein docking exploiting pairwise interfacial residue restraints

dc.contributor.author Xue, Li
dc.contributor.author Rodrigues, João
dc.contributor.author Dobbs, Drena
dc.contributor.author Dobbs, Drena
dc.contributor.author Honavar, Vasant
dc.contributor.author Bonvin, Alexandre
dc.contributor.department Genetics, Development and Cell Biology
dc.date 2018-02-18T05:16:45.000
dc.date.accessioned 2020-06-30T04:01:11Z
dc.date.available 2020-06-30T04:01:11Z
dc.date.copyright Fri Jan 01 00:00:00 UTC 2016
dc.date.issued 2016-01-01
dc.description.abstract <p>Although many advanced and sophisticated <em>ab initio</em> approaches for modeling protein–protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon–alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein–protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein–protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models.</p>
dc.description.comments <p>This article is from <em>Briefings in Bioinformatics </em>(2016), doi: <a href="https://doi.org/10.1093/bib/bbw027">10.1093/bib/bbw027</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/gdcb_las_pubs/120/
dc.identifier.articleid 1123
dc.identifier.contextkey 9801731
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath gdcb_las_pubs/120
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/37785
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/gdcb_las_pubs/120/2016_Dobbs_TemplateBased.pdf|||Fri Jan 14 19:10:22 UTC 2022
dc.source.uri 10.1093/bib/bbw027
dc.subject.disciplines Bioinformatics
dc.subject.disciplines Cell and Developmental Biology
dc.subject.disciplines Genetics and Genomics
dc.subject.keywords template-based modeling
dc.subject.keywords interface restrained docking
dc.subject.keywords CA-CA-guided docking
dc.subject.keywords AIR-guided docking
dc.subject.keywords refinement
dc.title Template-based protein–protein docking exploiting pairwise interfacial residue restraints
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 7e096c4f-9007-41e4-9414-989c3ea9bc88
relation.isOrgUnitOfPublication 9e603b30-6443-4b8e-aff5-57de4a7e4cb2
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