Next: Introduction
A PROLOG Approach to Analysing Protein Structure
Geoffrey J. Barton
and Christopher J. Rawlings
,
University of Oxford; Laboratory of Molecular Biophysics
The Rex Richards Building; South Parks Road; Oxford OX1 3QU - UK (geoff@uk.ac.ox.biop)
and
Biomedical Computing Unit;Imperial Cancer Research Fund
Lincoln's Inn Fields;London
keywords: logic programming, PROLOG, protein structure, secondary structure,
topology, relational database, knowledge base
Abstract:
This paper provides a detailed description of a database of protein structure implemented
in the logic programming language PROLOG. The database allows flexible access to
structural information at the atom, residue, secondary structure and topology levels of
the protein structural hierarchy. An extended version of the Kabsch and Sander algorithm
for secondary structure definition has been implemented in PROLOG, forming an integral
part of the database. For protein structure analysis, the PROLOG system shows significant
advantages in flexibility over conventional programming languages such as Fortran, and
Relational Database Managements Systems using SQL.