{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T03:57:31Z","timestamp":1778299051901,"version":"3.51.4"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Discovery of binding sites is important in the study of protein\u2013protein interactions. In this paper, we introduce stable and significant motif pairs to model protein-binding sites. The stability is the pattern\u2019s 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.<\/jats:p><jats:p>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.<\/jats:p><jats:p>Contact \u00a0haiquan@i2r.a-star.edu.sg<\/jats:p><jats:p>Supplementary information \u00a0http:\/\/sdmc.i2r.a-star.edu.sg\/BindingMotifPairs<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti019","type":"journal-article","created":{"date-parts":[[2004,9,17]],"date-time":"2004-09-17T00:13:37Z","timestamp":1095380017000},"page":"314-324","source":"Crossref","is-referenced-by-count":12,"title":["Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets"],"prefix":"10.1093","volume":"21","author":[{"given":"Haiquan","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2004,9,16]]},"reference":[{"key":"2023051305563366200_B1","unstructured":"Atteson, K. 1998Calculating the exact probability of language-like patterns in biomolecular sequences. 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