P3D-SQL: Extending oracle PL/SQL capabilities towards 3D protein structure similarity searching

Abstract

3D protein structure similarity searching is one of the most popular processes performed in the structural bioinformatics. The process is usually performed through dedicated websites or desktop software tools, which makes a secondary processing of the search results difficult. One of the alternatives is to store macromolecular data in relational databases and perform the similarity searching on the server-side of the client-server architecture. Unfortunately, relational database management systems (DBMSs) are not designed for efficient storage and processing of biological data, such as 3D protein structures. In this paper, we present the P3D-SQL extension to the Oracle PL/SQL language that allows invoking protein similarity searching in SQL queries and perform the process efficiently against a database of 3D protein structures. Availability: P3D-SQL is available from P3D-SQL project home page at: http://zti.polsl.pl/w3/dmrozek/science/p3dsql.htm.