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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti019
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 17, 2004
Revised June 8, 2004
Accepted September 2, 2004

Article

Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets

Haiquan Li 1* and Jinyan Li 2

1 Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore, 119613; School of Computing, National University of Singapore, Singapore, 119260
2 Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore, 119613

* To whom correspondence should be addressed. E-mail: haiquan{at}i2r.a-star.edu.sg.


  Abstract

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 PDB to help 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 literature were also used to confirm the effectiveness of our method.

Supplementary Information: http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs.


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