Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2003 | 10.1093/bioinformatics/btg278 | BIOINFORMATICS |
Keywords | Field | DocType |
monte carlo,protein family,molecular biology,chemokine receptor,distance matrix,search space | Similitude,Protein family,Monte Carlo method,Phylogenetic tree,Protein–protein interaction,Distance matrices in phylogeny,Computer science,Distance matrix,Bioinformatics,Phylogenetics | Journal |
Volume | Issue | ISSN |
19 | 16.0 | 1367-4803 |
Citations | PageRank | References |
23 | 2.49 | 0 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jason Gertz | 1 | 61 | 3.60 |
| Georgiy Elfond | 2 | 23 | 2.49 |
| Anna Shustrova | 3 | 23 | 2.83 |
| Matt Weisinger | 4 | 23 | 2.49 |
| Matteo Pellegrini | 5 | 173 | 18.42 |
| Shawn Cokus | 6 | 146 | 14.23 |
| Bruce Rothschild | 7 | 36 | 7.21 |