PDB id to DSSP

Question

[amir_zarghami_13]

Hi,I’m a masters student studying Bioinformatics, I’m new to the field. My problem is that I need to get the DSSP file for a large number of proteins, using their PDB ids. We have the PDB ids in an excel file. Thank you.

Answer 1

[Joe]

You can download secondary structure assignments at this page: https://www.rcsb.org/pdb/static.do?p=download/http/index.html#ss

In particular, scroll to the bottom to this link: https://cdn.rcsb.org/etl/kabschSander/ss.txt.gz

You can then query that fasta file for your PDB IDs.

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Here's another tip - don't use Excel.

Answer 2

[Mike]

You can download all pre-calculated DSSP files from this link...

https://swift.cmbi.umcn.nl/gv/dssp/

https://swift.cmbi.umcn.nl/gv/dssp/DSSP_5.html