Delineation and analysis of the conceptual data model implied by the "IUPAC Recommendations for Biochemical Nomenclature".

ABSTRACT: Computational analysis of the bonding, geometric, and topological relationships within proteins typically takes on the order of hours, mainly devoted to the writing of scripts and code to correctly parse the data. The Structured Query Language (SQL) built into modern database management systems eliminates the need for data parsing, effectively reducing the analysis time to seconds. To this end, we have formulated a conceptual data model (CDM) for proteins based on the IUPAC recommendations for biochemical nomenclature. This conceptual data model makes explicit the inherent bonding relationships between the atoms of a protein, as well as the geometric (bond angle and torsion angle) and topological (chirality) relationships between the bonds. The validity of the CDM has been tested with a re

SUBMITTER: Fox-Erlich S 

PROVIDER: S-EPMC2280010 | biostudies-literature | 2004 Sep

REPOSITORIES: biostudies-literature