TY - CHAP
T1 - Prediction of protein interactions by structural matching
T2 - Prediction of PPI networks and the effects of mutations on PPIs that combines sequence and structural information
AU - Tuncbag, Nurcan
AU - Keskin, Ozlem
AU - Nussinov, Ruth
AU - Gursoy, Attila
N1 - Publisher Copyright:
© Springer Science+Business Media LLC 2017.
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
KW - Mutation mapping
KW - PPI network
KW - PPI prediction
KW - Structural matching
KW - Structural pathway modeling
UR - http://www.scopus.com/inward/record.url?scp=85011556565&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-6783-4_12
DO - 10.1007/978-1-4939-6783-4_12
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C2 - 28150242
AN - SCOPUS:85011556565
T3 - Methods in Molecular Biology
SP - 255
EP - 270
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -