Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representationReport as inadecuate




Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation - Download this document for free, or read online. Document in PDF available to download.

Algorithms for Molecular Biology

, 2:12

First Online: 03 October 2007Received: 25 May 2007Accepted: 03 October 2007

Abstract

BackgroundSome 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.

ResultsWe 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.

ConclusionOur 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1748-7188-2-12 contains supplementary material, which is available to authorized users.

Download fulltext PDF



Author: Rodrigo Gouveia-Oliveira - Anders G Pedersen

Source: https://link.springer.com/







Related documents