Recent breakthroughs in high throughput experiments to determine protein-protein interaction have generated a vast amount of protein interaction data. However, most of the experiments could only answer the question of whether two proteins interact but not the question on the mechanisms by which proteins interact. Such understanding is crucial for understanding the protein interaction of an organism as a whole (the interactome) and even predicting novel protein interactions. Protein interaction usually occurs at some specific sites on the proteins and, given their importance, they are usually well conserved throughout the evolution of the proteins of the same family. Based on this observation, a number of works on finding protein patterns/motifs conserved in interacting proteins have emerged in the last few years. Such motifs are collectively termed as the interaction motifs. This chapter provides a review on the different approaches on finding interaction motifs with a discussion on their implications, potentials and possible areas of improvements in the future.
High throughput protein-protein interaction data: clues for the architecture of protein complexes
