Delineation and analysis of the conceptual data model implied by the “IUPAC Recommendations for Biochemical Nomenclature”

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 elim...

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Bibliographic Details
Published in:Protein science 2004-09, Vol.13 (9), p.2559-2563
Main Authors: Fox‐Erlich, Susan, Martyn, Timothy O., Ellis, Heidi J.C., Gryk, Michael R.
Format: Article
Language:English
Subjects:
Biochemical Phenomena
Biochemistry
conceptual data model
Databases, Protein
For the Record
IUPAC
Models, Molecular
Protein Conformation
protein structure
relational database
Societies, Scientific
Software
Terminology as Topic
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Summary: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 reduced implementation using commercial database software. The ease in both populating the database with data from the Protein Data Bank and formulating/executing queries supports the correctness of the model. The ability to conduct truly interactive analyses of protein structure is essential to fully capitalize on the explosion in postgenomic protein structure data.
ISSN:0961-8368
1469-896X
DOI:10.1110/ps.04810204