title: Deriving an amino acid distance matrix.
abstract: Various methods were investigated to convert an amino acid similarity matrix into a low-dimensional, metric distance matrix. Using projection techniques, no unique transformation was found and of the many inversion forms investigated, simple negation normalized by the diagonal elements produced a good fit to the original data. An inter-row distance also gave a comparable fit and when evaluated by weighted least-squares minimization was found to be preferable. A rank-ordered form of the matrices was also derived by constraining neighbours to be equidistant in 3D-space. This produced a network configuration not unlike that produced in a previous analysis of amino acid physicochemical properties. The derived forms might find applications in sequence alignment, including pattern-matching algorithms, and the construction of phylogenetic trees.
authors.affiliation: Laboratory of Mathematical Biology, National Institute for Medical Research, Ridgeway, London, U.K.
authors.forename: W R
authors.initials: WR
authors.lastname: Taylor
authors.forename: D T
authors.initials: DT
authors.lastname: Jones
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D008433:Mathematics; D008956:Models, Chemical; D008968:Molecular Conformation
chemical_list: D000596:Amino Acids