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Algorithms Mol Biol. 2007 Oct 3;2:12.

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.

Author information

1
Center for Biological sequence analysis, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark. rodrigo@cbs.dtu.dk

Abstract

BACKGROUND:

Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues - coevolution. Our goal is to find these coevolving residues.

RESULTS:

We present six new methods for detecting coevolving residues. Among other things, we suggest measures that are variants of Mutual Information, and measures that use a multidimensional representation of each residue in order to capture the physico-chemical similarities between amino acids. We created a benchmarking system, in silico, able to evaluate these methods through a wide range of realistic conditions. Finally, we use the combination of different methods as a way of improving performance.

CONCLUSION:

Our best method (Row and Column Weighed Mutual Information) has an estimated accuracy increase of 63% over Mutual Information. Furthermore, we show that the combination of different methods is efficient, and that the methods are quite sensitive to the different conditions tested.

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