title: Domain-mediated protein interaction prediction: From genome to network.
abstract: Protein-protein interactions (PPIs), involved in many biological processes such as cellular signaling, are ultimately encoded in the genome. Solving the problem of predicting protein interactions from the genome sequence will lead to increased understanding of complex networks, evolution and human disease. We can learn the relationship between genomes and networks by focusing on an easily approachable subset of high-resolution protein interactions that are mediated by peptide recognition modules (PRMs) such as PDZ, WW and SH3 domains. This review focuses on computational prediction and analysis of PRM-mediated networks and discusses sequence- and structure-based interaction predictors, techniques and datasets for identifying physiologically relevant PPIs, and interpreting high-resolution interaction networks in the context of evolution and human disease.
authors.affiliation: The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada. Juri.Reimand@utoronto.ca
authors.forename: Jüri
authors.initials: J
authors.lastname: Reimand
authors.forename: Shirley
authors.initials: S
authors.lastname: Hui
authors.forename: Shobhit
authors.initials: S
authors.lastname: Jain
authors.forename: Brian
authors.initials: B
authors.lastname: Law
authors.forename: Gary D
authors.initials: GD
authors.lastname: Bader
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D016678:Genome; D006801:Humans; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D018909:src Homology Domains
chemical_list: D010455:Peptides; D011506:Proteins; D004247:DNA