PDB@: An offline toolkit for exploration and analysis of PDB files
- 283 Downloads
Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.
KeywordsPDB Heat map RMSD Protein–protein interactions Mechanize and ClustalW
We thank SASTRA University for providing us with a wonderful infrastructure to successfully complete our research. We also thank Dr. M. Vijayalakshmi for her support and motivation. We thank Dr. S. Thamodaran, Dr. K. Saraboji and Dr. N.T. Saraswathi for their valuable ideas.
- 2.Conscript: RasMol to PyMOL script converter (2010) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134254/ Accessed 13 Nov 2012
- 3.RAMPAGE: Ramachandran Plot Analysis Server (2010) Crystallography and Biology Group, University of Cambridge, Department of Biochemistry, http://mordred.bioc.cam.ac.uk/~rapper/rampage.php Accessed 22 Nov 2012
- 4.Protein interactions and properties explorer (2011) IBI Biosolutions, INDIA. http://pipe.ibibiosolutions.com/ Accessed 11 Nov 2012
- 8.Fasman GD, Sober HA (1976) Handbook of biochemistry and molecular biology: physical and chemical data, miscellaneous, 3rd edn. CRC Press, ClevelandGoogle Scholar