Monday, February 11, 2008

Protein 3D structure analysis

I was trying to find today programs for analyzing protein 3D structures .. A rare art
new generation of Bioinformaticians may never learnt. Especially, I wanted to calculate secondary structure, solvent accessibility, hydrogen bonds, torsion angles and residue packings from protein 3D structures.

Any ways, the old programs viz. Comparer, JOY suite (people believe its no fun at all running it) at the University of Cambridge and WHAT IF are still under copyrights that you still have to FAX them to get a license. (aka long wait .....)

I finally downloaded DSSP (CMBI version), STRIDE (from EMBL/EBI) and PSA (sali lab). Also, I will try VADAR suite of algorithms from Canada and PROMOTIF (I never used it before though) to get most of the required information.

Let's see where these guys take me !! Anybody who want to write Bioperl modules for them :D !!!

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