New methods to measure residues coevolution in proteins.

ABSTRACT:

Background

The covariation of two sites in a protein is often used as the degree of their coevolution. To quantify the covariation many methods have been developed and most of them are based on residues position-specific frequencies by using the mutual information (MI) model.

Results

In the paper, we proposed several new measures to incorporate new biological constraints in quantifying the covariation. The first measure is the mutual information with the amino acid background distribution (MIB), which incorporates the amino acid background distribution into the marginal distribution of the MI model. The modification is made to remove the effect of amino acid evolutionary pressure in measuring covariation. The second measure is the mutual information of residues physicochemic

SUBMITTER: Gao H 

PROVIDER: S-EPMC3123609 | biostudies-literature | 2011 May

REPOSITORIES: biostudies-literature