How to find the percentage of secondary structure of a protein from a .PDB file?

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Hiqmet Kamberaj

You can use the STRIDE program implemented in VMD package. For that, you will need to have the PDB coordinates. It is not going to give you the percentage numerically (in %), but you may still be able to determine it from the graphs, by estimating the number of residues forming each secondary structure.

Reference: Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.

Woonghee Lee

STRIDE web server is here:

http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py

You can upload PDB file and simply count secondary structures assigned to residues.