Inferring protein interactions from phylogenetic distance matrices

被引:52
作者
Gertz, J
Elfond, G
Shustrova, A
Weisinger, M
Pellegrini, M
Cokus, S
Rothschild, B
机构
[1] Cornell Univ, Dept Math, Ithaca, NY 14853 USA
[2] Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA
[3] Div Engn & Appl Sci, Cambridge, MA 02138 USA
[4] Prot Pathways, Woodland Hills, CA USA
[5] Univ Calif Los Angeles, Dept Math, Los Angeles, CA 90024 USA
基金
美国国家科学基金会;
关键词
D O I
10.1093/bioinformatics/btg278
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Finding the interacting pairs of proteins between two different protein families whose members are known to interact is an important problem in molecular biology. We developed and tested an algorithm that finds optimal matches between two families of proteins by comparing their distance matrices. A distance matrix provides a measure of the sequence similarity of proteins within a family. Since the protein sets of interest may have dozens of proteins each, the use of an efficient approximate solution is necessary. Therefore the approach we have developed consists of a Metropolis Monte Carlo optimization algorithm which explores the search space of possible matches between two distance matrices. We demonstrate that by using this algorithm we are able to accurately match chemokines and chemokine-receptors as well as the tgfbeta family of ligands and their receptors.
引用
收藏
页码:2039 / 2045
页数:7
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