Prediction of protein interactions by structural matching: Prediction of PPI networks and the effects of mutations on PPIs that combines sequence and structural information

Nurcan Tuncbag, Ozlem Keskin*, Ruth Nussinov, Attila Gursoy

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

5 Scopus citations

Abstract

Structural details of protein interactions are invaluable to the understanding of cellular processes. However, the identification of interactions at atomic resolution is a continuing challenge in the systems biology era. Although the number of structurally resolved complexes in the Protein Databank increases exponentially, the complexes only cover a small portion of the known structural interactome. In this chapter, we review the PRISM system that is a protein–protein interaction (PPI) prediction tool—its rationale, principles, and applications. We further discuss its extensions to discover the effect of single residue mutations, to model large protein assemblies, to improve its performance by exploiting conformational protein ensembles, and to reconstruct large PPI networks or pathway maps.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages255-270
Number of pages16
DOIs
StatePublished - 2017

Publication series

NameMethods in Molecular Biology
Volume1558
ISSN (Print)1064-3745

Funding

FundersFunder number
TUBITAK projects113E164, 114M196
TUBITAK-Marie Curie Co-funded Brain Circulation Scheme114C026
National Institutes of HealthHHSN261200800001E
National Cancer InstituteZIABC010442
Frederick National Laboratory for Cancer Research
Bilim Akademisi

    Keywords

    • Mutation mapping
    • PPI network
    • PPI prediction
    • Structural matching
    • Structural pathway modeling

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