title: Usability of the kink parameters for nucleic acid structure in database.
abstract: DNA/RNA molecules with the specific three-dimensional structure, express the specific structural and biological functions. The knowledge integration based on three dimensional structures can be used to explain biochemical observations, to predict biological functions and to design drugs specific to a given complex system. The database cataloging the interaction motifs of nucleic acid moieties has been developed. Skew matrix, a kind of kink parameter, affords the structural description between the adjacent moieties. The proper values in skew matrix have the good properties, i.e., impregnable and flexible presentation. The geometrical parameters about hydrogen bond and base stacking would also provide the tolerant aspect for stereochemical bioinformatics. The tentative database including these parameters with the species and physical properties of the surrounding nucleic acid components and amino acids has been constructed.
authors.affiliation: School of Pharmaceutical Sciences, University of Sizuoka, 52-1 Yada, Suruga-ku, Shizuoka-shi, Shizuoka 422-8526, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fujii
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D030561:Databases, Nucleic Acid; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation
chemical_list: D000596:Amino Acids