Finding obsolete pdb entries

From: Simon Kolstoe
Date: 24 August 2011 11:14

Dear ccp4bb,

About 6 years ago I noted a couple of structures I was interested in were removed from the pdb. I saw in a recent email discussion that it is possible to access obsolete entries, however unfortunately I do not have the pdb code of the structure I am interested in - and neither does the original publication list the pdb code. Is there a way of searching withdrawn/obsolete entries for author name, macromolecule etc. or are structures that were withdrawn over 5 years ago lost for good?

Thanks,

Simon

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From: Gerard DVD Kleywegt

!Hola! Actually, you can. Tom Oldfield has written a web interface to query the PDBe search database directly using SQL - it lives here:

    http://www.ebi.ac.uk/pdbe-as/pdbedatabase/

If you want to look for obsoleted entries by molecule name, paste the following into the SQL box:

Select * from pdb_status WHERE status_code in ('OBS')  and
upper(TITLE) like '%ISOMERASE%';

Hit the "Submit SQL" button and you will get a list of hits with the word "ISOMERASE" in their title. Hit the "Get" (Text) button to save the complete list of hits.

If you know one of the authors, try the following query instead:

Select * from pdb_status WHERE status_code in ('OBS')  and
upper(AUTHOR_LIST) like '%JONES%';

!No hay de que!

--Gerard