title: Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs.
authors.affiliation: Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613. haiquan@i2r.a-star.edu.sg
authors.forename: Haiquan
authors.initials: H
authors.lastname: Li
authors.forename: Jinyan
authors.initials: J
authors.lastname: Li
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000032:analysis* / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins