Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners

• Published in: PLoS computational biology Vol. 3; no. 4; p. e43
• Main Authors: Shoemaker, Benjamin A, Panchenko, Anna R
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.04.2007; Public Library of Science (PLoS)
• Subjects: Algorithms; Binding Sites; Computational Biology; Computer Simulation; Computer-generated environments; Education; Genes; Genetics; Genomes; Hypotheses; Methods; Models, Chemical; Molecular Biology; None; Phylogenetics; Protein Binding; Protein Interaction Mapping - methods; Protein Structure, Tertiary; Protein-protein interactions; Proteins; Proteins - chemistry; Proteins - metabolism; Sequence Analysis, Protein - methods; Studies; United States; Protein Structure, Tertiary; Proteins; Sequence Analysis, Protein; Algorithms; Models, Chemical; Computer Simulation; Protein Binding; Binding Sites; Protein Interaction Mapping
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.0030043

Recent advances in high-throughput experimental methods for the identification of protein interactions have resulted in a large amount of diverse data that are somewhat incomplete and contradictory. As valuable as they are, such experimental approaches studying protein interactomes have certain limitations that can be complemented by the computational methods for predicting protein interactions. In this review we describe different approaches to predict protein interaction partners as well as highlight recent achievements in the prediction of specific domains mediating protein-protein interactions. We discuss the applicability of computational methods to different types of prediction problems and point out limitations common to all of them.