[BiO BB] SCOP ids from PDB id

Goel, Manisha MAG at Stowers-Institute.org
Thu Jun 22 10:19:15 EDT 2006

Hi Pankaj,

If you really have only a few PDB ids.. you could go to SCOP site and
put them in the "Keyword search for SCOP entries" .. it will take you to
the scop entry for the respective PDB files.

The RCSB (PDB) site also gives you an option making the tabulated
report.. you could choose the options of "SCOP domain" for all the PDB
files of your interest and then look at the report.

Also, not a very elegant option but something that I tried for a larger
number of PDBids is to download the SCOP parseable file and write a
small script to "grep" for each pdb-id in this file.. It will come up
with the scop_id for each file..

Hopefully somebody else on the list will have a better method for
generating this result.
I could try to help if you wnat to try any of the above three options.

All the best !

PostDoctoral Associate
Stowers Institute for Medical Research
Kansas city, MO -64110

-----Original Message-----
bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformat
ics.org] On Behalf Of Pankaj
Sent: Thursday, June 22, 2006 5:56 AM
To: bio; bioperl
Subject: [BiO BB] SCOP ids from PDB id

Hi all,
I have a few PDB ids.
I want to know whether these structures are related or not.
One way was to do it by calculating RMSD among all of them and seeing if
they r related or not. Other way was to get their SCOP id's and comapre
if they belong to same SCOP family. My question is given a PDB id, how
do I get its SCOP id? Thanking all in advance,

Pankaj Khurana
Research Scholar
National Institute of Immunology
New Delhi
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