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: sekar@physics.iisc.ernet.in and sekar@serc.iisc.ernet.in) 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/.