Scoring residue conservation
Article first published online: 30 MAY 2002
Copyright © 2002 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 48, Issue 2, pages 227–241, 1 August 2002
How to Cite
Valdar, W. S.J. (2002), Scoring residue conservation. Proteins, 48: 227–241. doi: 10.1002/prot.10146
- Issue published online: 30 MAY 2002
- Article first published online: 30 MAY 2002
- Manuscript Accepted: 22 FEB 2002
- Manuscript Received: 12 OCT 2001
- protein sequence analysis;
- amino acid;
- evolutionary conservation;
- multiple sequence alignment
The importance of a residue for maintaining the structure and function of a protein can usually be inferred from how conserved it appears in a multiple sequence alignment of that protein and its homologues. A reliable metric for quantifying residue conservation is desirable. Over the last two decades many such scores have been proposed, but none has emerged as a generally accepted standard. This work surveys the range of scores that biologists, biochemists, and, more recently, bioinformatics workers have developed, and reviews the intrinsic problems associated with developing and evaluating such a score. A general formula is proposed that may be used to compare the properties of different particular conservation scores or as a measure of conservation in its own right. Proteins 2002;48:227–241. © 2002 Wiley-Liss, Inc.