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

Haiquan Li, Jinyan Li

Research output: Contribution to journalArticle

14 Citations (Scopus)

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 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.

Original languageEnglish (US)
Pages (from-to)314-324
Number of pages11
JournalBioinformatics
Volume21
Issue number3
DOIs
StatePublished - Feb 1 2005
Externally publishedYes

Fingerprint

Proteins
Protein
Interaction
Binding sites
Binding Sites
Protein-protein Interaction
Comparison Result
Iterative Process
Protein Binding
Computational complexity
Computational Complexity
Datasets
Databases
Model

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets. / Li, Haiquan; Li, Jinyan.

In: Bioinformatics, Vol. 21, No. 3, 01.02.2005, p. 314-324.

Research output: Contribution to journalArticle

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