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Domain‐mediated protein interaction prediction: From genome to network
Author(s) -
Reimand Jüri,
Hui Shirley,
Jain Shobhit,
Law Brian,
Bader Gary D.
Publication year - 2012
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2012.04.027
Subject(s) - pdz domain , computational biology , context (archaeology) , genome , protein–protein interaction , interaction network , domain (mathematical analysis) , human genome , sequence (biology) , computer science , protein interaction networks , biology , gene , genetics , mathematical analysis , paleontology , mathematics
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.