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Understanding protein-protein interactions: from domain level to motif level. (English) Zbl 1269.92040

Feng, Jiafeng (ed.) et al., Networks: from biology to theory. Selected papers based on the presentations at the conference, Sino-German Centre, Beijing, China. London: Springer (ISBN 978-1-84628-485-4/hbk). 229-247 (2007).
Summary: Understanding protein functional interactions is an important research focus in the post-genomic era. The identification of interacting motif pairs is essential for exploring the mechanism of protein interactions. We describe a word counting approach for discovering motif pairs from known interactions and pairs of proteins that are putatively not to interact. Our interacting motif pairs are validated by multiple-chain PDB structures and motif pairs extracted from PDB structures. The motif pairs are used to predict interactions between proteins by three different methods. For all the methods used, our predicted protein-protein interactions significantly overlap with the experimental physical interactions. Furthermore, the mean correlation coefficients of the gene expression profiles for our predicted protein pairs are significantly higher than that for random pairs. Supplementary materials are available online at http://ctb.pku.edu.cn/{^}yuhuan.
For the entire collection see [Zbl 1116.92002].

MSC:

92C40 Biochemistry, molecular biology
92-08 Computational methods for problems pertaining to biology
68R15 Combinatorics on words

Software:

IntAct; PROSITE
PDFBibTeX XMLCite
Full Text: DOI