title: A new method for analyzing protein sequence relationships based on Sammon maps.
abstract: 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.
authors.affiliation: 3-Dimensional Pharmaceuticals, Inc., Exton, Pennsylvania 19341, USA. dimitris@dp.com
authors.forename: D K
authors.initials: DK
authors.lastname: Agrafiotis
mesh_terms: D000465:Algorithms; D011494:Protein Kinases / Q000737:chemistry; D017421:Sequence Analysis / Q000379:methods*
chemical_list: D011494:Protein Kinases