Using Fixed Point Theorems to Model the Binding in Protein-Protein Interactions
IEEE Transactions on Knowledge and Data Engineering
| Hi-index | 3.84 |
Motivation: Discovery of binding sites is important in the study of protein--protein interactions. In this paper, we introduce stable and significant motif pairs to model protein-binding sites. The stability is the pattern's resistance to some transformation. The significance is the unexpected frequency of occurrence of the pattern in a sequence dataset comprising known interacting protein pairs. Discovery of stable motif pairs is an iterative process, undergoing a chain of changing but converging patterns. Determining the starting point for such a chain is an interesting problem. We use a protein complex dataset extracted from the Protein Data Bank to help in identifying those starting points, so that the computational complexity of the problem is much released. Results: We found 913 stable motif pairs, of which 765 are significant. We evaluated these motif pairs using comprehensive comparison results against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method. Contact haiquan@i2r.a-star.edu.sg Supplementary information http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs