Bioinformatics Advance Access originally published online on September 16, 2004
Bioinformatics 2005 21(3):314-324; doi:10.1093/bioinformatics/bti019
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
1 Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613
2 School of Computing, National University of Singapore Singapore 119260
*To whom correspondence should be addressed.
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{at}i2r.a-star.edu.sg
Supplementary information http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs
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