Understanding Protein-Protein Interactions: From Domain Level to Motif Level

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.