Format

Send to

Choose Destination
See comment in PubMed Commons below
Bioinformatics. 2005 Nov 15;21(22):4116-24. Epub 2005 Sep 13.

Using information theory to search for co-evolving residues in proteins.

Author information

  • 1Department of Applied Mathematics, University of Western Ontario, London, Canada.

Abstract

MOTIVATION:

Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). However important residues may also mutate, with compensatory mutations occurring elsewhere in the protein, which serve to preserve or restore functionality. It is difficult to distinguish these co-evolving sites from other non-conserved sites.

RESULTS:

We used Mutual Information (MI) to identify co-evolving positions. Using in silico evolved MSAs, we examined the effects of the number of sequences, the size of amino acid alphabet and the mutation rate on two sources of background MI: finite sample size effects and phylogenetic influence. We then assessed the performance of various normalizations of MI in enhancing detection of co-evolving positions and found that normalization by the pair entropy was optimal. Real protein alignments were analyzed and co-evolving isolated pairs were often found to be in contact with each other.

AVAILABILITY:

All data and program files can be found at http://www.biochem.uwo.ca/cgi-bin/CDD/index.cgi

PMID:
16159918
DOI:
10.1093/bioinformatics/bti671
[PubMed - indexed for MEDLINE]
Free full text
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Silverchair Information Systems Icon for HighWire
    Loading ...
    Support Center