title: Predicting Protein-Protein Interactions from the Molecular to the Proteome Level.
abstract: Identification of protein-protein interactions (PPIs) is at the center of molecular biology considering the unquestionable role of proteins in cells. Combinatorial interactions result in a repertoire of multiple functions; hence, knowledge of PPI and binding regions naturally serve to functional proteomics and drug discovery. Given experimental limitations to find all interactions in a proteome, computational prediction/modeling of protein interactions is a prerequisite to proceed on the way to complete interactions at the proteome level. This review aims to provide a background on PPIs and their types. Computational methods for PPI predictions can use a variety of biological data including sequence-, evolution-, expression-, and structure-based data. Physical and statistical modeling are commonly used to integrate these data and infer PPI predictions. We review and list the state-of-the-art methods, servers, databases, and tools for protein-protein interaction prediction.
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
authors.affiliation: Graduate School of Informatics, Department of Health Informatics, Middle East Technical University , 06800 Ankara, Turkey.
authors.forename: Nurcan
authors.initials: N
authors.lastname: Tuncbag
authors.forename: Attila
authors.initials: A
authors.lastname: Gursoy
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D057225:Data Mining; D030562:Databases, Protein / Q000706:statistics & numerical data*; D015870:Gene Expression; D006801:Humans; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods* / Q000706:statistics & numerical data; D020543:Proteome / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D020543:Proteome