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Protein Science, Vol 6, Issue 2 287-293, Copyright © 1997 by Cold Spring Harbor Laboratory Press

ARTICLE

A new method for analyzing protein sequence relationships based on Sammon maps

D. K. AGRAFIOTIS
3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Suite 104, Exton, Pennsylvania 19341

Recent advances in gene sequencing and rational drug design have re-emphasized the need for new methods for protein analysis, classification, and structure and function prediction. In this article, we introduce a new method for analyzing protein sequences based on Sammon's non-linear mapping algorithm. When applied to a family of homologous sequences, the method is able to capture the essential features of the similarity matrix, and provides a faithful representation of chemical or evolutionary distance in a simple and intuitive way. The merits of the new algorithm are demonstrated using examples from the protein kinase family.
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