Is there any webserver or software thorough which i can calculate the percentage of secondary structure ( % of alpha helix, % if beta sheet etc). Other than Gromacs which require xtc file. I have only protein structure in pdb format.
There is supposedly PDBSum to do this: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
I have done it on the Klenow fragment (PDB: 1KLN) and I don't think its calculations are correct for number of alpha helices. I don't trust it. Secondary structure of proteins is computed from the Ramachandran phi and psi angles of the neighboring residues in sequence.
if you don't need to compute secondary structure in high throughput but just for a few structures, I would do it sort of manually in Pymol.
#Hashtags are comments.
Open Pymol > File > Open PDB
Click the colorful "C" for color > by ss # for secondary structure.
Type: set seq_view, on # to display sequence:
Type: select helices, ss H # for helices
Type: select sheets, ss S # for beta sheets
Type select loops, ss l+ # for loops
Scroll through the sequence and count the colored helices and loops. The protein is already colored by secondary structure so it is easy to imagine how many there are.
Percentage of alpha helices = [(number of alpha helices) / (number of alpha helices + number of beta sheets + number of loops)] * 100%
Pymol can actually give you a ramachandran plot with
type: rama # but don't click on any of the points or you actually drag the atoms around in space.
Anytime you have a PDB file there may be more than one chain up to like 8 chains for crystal lattice symmetry. If all the chains have the same sequence then it is the same protein packed tightly in the crystal lattie so delete or hide the other chains.
Using VMD, load your protein.pdb in the GUI, then:
Extensions > Analysis > Sequence Viewer
You can find different color coding for helix 'H' and so on. Manually you can calculate such as:
= (Total number of 'H')/(Total number of residues in your protein.pdb).
OR
You can work on Tcl/Tkl script to to the same calculation.
Hope this helps!
Best
Shubhashree
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