DocumentCode :
983772
Title :
Using fixed point theorems to model the binding in protein-protein interactions
Author :
Li, Jinyan ; Li, Haiquan
Author_Institution :
Inst. for Infocomm Res., Heng Mui Keng Terrace, Singapore
Volume :
17
Issue :
8
fYear :
2005
Firstpage :
1079
Lastpage :
1087
Abstract :
The binding in protein-protein interactions exhibits a kind of biochemical stability in cells. The mathematical notion of fixed points also describes stability. A point is a fixed point if it remains unchanged after a transformation by a function. Many points may not be a fixed point, but they may approach a stable status after multiple steps of transformation. In this paper, we define a point as a protein motif pair consisting of two traditional protein motifs. We propose a function and propose a method to discover stable motif pairs of this function from a large protein interaction, sequence data set. There are many interesting properties for this function (for example, the convergence). Some of them are useful for gaining much efficiency in the discovery of those stable motif pairs; some are useful for explaining why our proposed fixed point theorems are a good way to model the binding of protein interactions. Our results are also compared to biological results to elaborate the effectiveness, of our method.
Keywords :
biology computing; data mining; genetics; proteins; biochemical stability; bioinformatics; fixed point theorem; genome; mining methods; protein motif pair; protein-protein interaction; Amino acids; Biochemistry; Bioinformatics; Convergence; DNA; Genomics; Nuclear magnetic resonance; Proteins; Sequences; Stability; Index Terms- Bioinformatics (genome or protein) database; biology and genetics.; generating functions; mining methods and algorithms; stability and instability;
fLanguage :
English
Journal_Title :
Knowledge and Data Engineering, IEEE Transactions on
Publisher :
ieee
ISSN :
1041-4347
Type :
jour
DOI :
10.1109/TKDE.2005.134
Filename :
1458701
Link To Document :
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