parse http://www.rcsb.org/pdb/files/ss.txt

Each PDB has records that define your ss elements. Write a PERL script to mach your mapping region to the residue positions defined in these records. The challenge would be to scan through that short stretch through PDB-NR. Develop an algorithm to do this in 2 steps.

Something like this?

http://www.rcsb.org/pdb/staticHelp.do?p=help/advancedsearch/sequenceMotif.html

Or you can carry out a PHI-BLAST search against a suitable database (the PDB if you are interested in empirically-confirmed secondary structure annotations):

http://www.ncbi.nlm.nih.gov/blast/html/PHIsyntax.html

Then you can just parse the PDB matches to read the secondary structure records from the respective PDB files (or you can use something like DSSP to reassign them).

However, if you use the PDB you should be aware of two potential caveats (depending on the kind of analysis you want to carry out):

1.- There may be more than one structure for each protein and therefore you will need to remove redundancy prior to compute your statistics.

2.- The PDB is biased towards proteins that are amenable to crystallisation.

I am not aware of a database with precomputed secondary structure annotations (but maybe it exists...). Most databases such as UniProtKB contain empirical secondary structure annotations when available.

Thank you all.

Your answers make it quite possible for me. I need to spend some time on it.

Thank you again for sparing your time.

parse http://www.rcsb.org/pdb/files/ss.txt

Dear Lukasz,

Thank you very much.

Best,

Jogender

Check SecBase, an extensio to ReLiBase,

a parsable database interface for the whole pdb.

J Chem Inf Model. 2009 Oct;49(10):2388-402. doi: 10.1021/ci900202d.

Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

Koch O1, Cole J, Block P, Klebe G.

Here

Download the PDB and parse the files using PyMol and a Python script. Should be fairly easy to to. PyMol has quite a few commands you can use, like getting the secondary structure of an amino acid within the structure etc.

You can also try out this using Schrodinger software.

Thank you all for your suggestions.

Your way of approach may not yield correct result. Existence of domains with 31.45% of carbon in structure determine the secondary structures. For example a wild type protein with certain stretch of alpha form is mutated with 100th position away from the stretch is got modified in the helix form. So the stretch is not deciding the secondary structures but carbon domains.