In silico recognition of protein-protein interactions: Theory and applications

Byung Hoon Park, Phuongan Dam, Chongle Pan, Ying Xu, Al Geist, Grant Heffelfinger, Nagiza F. Samatova

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Protein-protein interactions are fundamental to cellular processes. They are responsible for phenomena like DNA replication, gene transcription, protein translation, regulation of metabolic pathways, immunologic recognition, signal transduction, etc. The identification of interacting proteins is therefore an important prerequisite step in understanding their physiological functions. Due to the invaluable importance to various biophysical activities, reliable computational methods to infer protein-protein interactions from either structural or genome sequences are in heavy demand lately. Successful predictions, for instance, will facilitate a drug design process and the reconstruction of metabolic or regulatory networks. In this chapter, we review: (a) high-throughput experimental methods for identification of protein-protein interactions, (b) existing databases of protein-protein interactions, (c) computational approaches to predicting protein-protein interactions at both residue and protein levels, (d) various statistical and machine learning techniques to model protein-protein interactions, and (e) applications of protein-protein interactions in predicting protein functions. We also discuss intrinsic drawbacks of the existing approaches and future research directions.

Original languageEnglish
Title of host publicationAdvanced Data Mining Technologies in Bioinformatics
PublisherIGI Global
Pages248-268
Number of pages21
ISBN (Print)9781591408635
DOIs
StatePublished - 2006

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