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.
Publication types
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Comparative Study
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Evaluation Study
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Research Support, U.S. Gov't, Non-P.H.S.
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Validation Study
MeSH terms
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Algorithms*
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Amino Acid Sequence
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Binding Sites
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Chemokines / chemistry
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Chemokines / genetics
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Chromosome Mapping / methods*
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Cluster Analysis
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Conserved Sequence
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Gene Expression Profiling / methods*
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Molecular Sequence Data
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Monte Carlo Method
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Phylogeny*
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Protein Binding / genetics
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Protein Interaction Mapping / methods*
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Proteins / chemistry*
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Proteins / genetics*
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Receptors, Chemokine / chemistry
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Receptors, Chemokine / genetics
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Receptors, Transforming Growth Factor beta / chemistry
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Receptors, Transforming Growth Factor beta / genetics
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Sequence Alignment / methods
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Sequence Analysis, Protein / methods*
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Sequence Homology, Amino Acid
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Transforming Growth Factor beta / chemistry
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Transforming Growth Factor beta / genetics
Substances
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Chemokines
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Proteins
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Receptors, Chemokine
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Receptors, Transforming Growth Factor beta
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Transforming Growth Factor beta