Scoring residue conservation


  • William S.J. Valdar

    Corresponding author
    1. Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, London, United Kingdom
    • Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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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.