Sap - Structure Analysis Package

SAP - Structure Analysis Package B. Balamurugan 1,$, M.N.A. Md. Roshan 1,$, B. Shaahul Hameed 1,$, K. Sumathi 1,$, K.N. Selvakumar 1,$, M. Jaikumar 1,$, T. Brindha 1,$, C. Vasuki Ranjani 1,$, Daliah Michael 1,$ and K. Sekar 1,2,* 1 Bioinformatics Centre 2 Supercomputer Education and Research Centre Indian Institute of Science Bangalore 560 012, India * To whom correspondence should be addressed (Email: [email protected] and [email protected]) Tel : +91-080-22933059 and 22932469 Fax : +91-080-23600085 and 23600551 Structure Analysis Package (SAP), a computing engine is developed to calculate and display various structural and functional regions in the three-dimensional protein structures available in the Protein Data Bank. To activate the engine, user needs to provide the PDB-id code of interest available in the Protein Data Bank or upload the three-dimensional atomic coordinates from the client machine through the web-browser. Results: The computing engine unravels the various structural and functional behavior embedded in the three-dimensional protein structures. The molecular graphics program, RASMOL is deployed to visualize the structural features graphically in the client machine. Several sequence databases like SWISS-PROT, PIR and genome sequences and non-redundant (25% and 90%) protein structures are interfaced with the computing engine. The various options provided in the computing engine are self-explanatory. Conclusion: The computing engine, SAP, is created and best optimized to delineate various user-interested structural features present in the chosen three-dimensional protein structure. The options provided in the computing engine are to better serve researchers working in the area of structural biology and structural bioinformatics. The web-server is available online over the World Wide Web interface at the URL http://iris.physics.iisc.ernet.in/sap/.