SAP - Structure Analysis Package

Kanagaraj Sekar
Bioinformatics Centre
(Centre of Excellence in Structural Biology and Biocomputing)
Supercomputer Education and Research Centre
Indian Institute of Science
Bangalore 560 012
India

In the post genome era, understanding various hidden structural features embedded in the protein molecule is of considerable interest in order to unravel its structural and functional behavior. Importantly, identifying and visualizing various structural features is an essential component for structural biologists and the process enhances creative thinking. On the whole, extracting essential knowledge from the protein structures is extremely important.  Towards this end, a computing engine, Structure Analysis Package (SAP), has been developed to calculate and display various structural and functional regions in the protein structures. For visualization, the free molecular graphics program, RASMOL, is deployed with the computing engine. The proposed computing engine is interfaced with the local copy of the Protein Data Bank and to activate, users need to provide the PDB-id code for the structures available in the Protein Data Bank or upload the three-dimensional atomic coordinates (Protein Data Bank format) from the client machine. The atomic coordinates are being updated every week from the RCSB-PDB server and hence the users can access all the structures available in the Protein Data Bank.  Various options implemented in the computing engine will be presented.

Keywords:  Information Retrieval, Knowledge Discovery, Internet computing, Protein Structures and Structural biology