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 language | English (US) |
|---|---|
| Pages (from-to) | 314-324 |
| Number of pages | 11 |
| Journal | Bioinformatics |
| Volume | 21 |
| Issue number | 3 |
| DOIs | |
| State | Published - Feb 1 2005 |
| Externally published | Yes |
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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 journal › Article
}
TY - JOUR
T1 - Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
AU - Li, Haiquan
AU - Li, Jinyan
PY - 2005/2/1
Y1 - 2005/2/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=13844250629&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=13844250629&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/bti019
DO - 10.1093/bioinformatics/bti019
M3 - Article
C2 - 15374856
AN - SCOPUS:13844250629
VL - 21
SP - 314
EP - 324
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 3
ER -