[Bioperl-l] PDB Parser

Bernd Mueller bernd at kirx.de
Mon Aug 20 16:57:28 UTC 2007


Maybe you wanna try the Database-EUtilities module from bioperl. They 
are described on http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

I tried them for a similar search on pubmed but without any reasonable 
results because my target was too focused.

 From EUtilities documentation on 

"Protein Database

The Protein database contains sequence data from the translated coding 
regions from DNA sequences in GenBank, EMBL, and DDBJ as well as protein 
sequences submitted to Protein Information Resource (PIR), SWISS-PROT, 
Protein Research Foundation (PRF), and Protein Data Bank (PDB) 
(sequences from solved structures). "

So PDB is included in eutilities from NCBI.


neeti somaiya wrote:
> Thanks for your response.
> Actually I am looking for something standalone and not on the web, as in
> something which I can download onto my machine and parse later to get id and
> title.
> On 8/20/07, Oliver Wafzig <Oliver.Wafzig at sygnis.de> wrote:
>> On Monday 20 August 2007 06:33, neeti somaiya wrote:
>>> Another question I had was, I am interested only in pdb id and title,
>> and
>>> for this I am downloading and unzipping each of the full pdb structure
>>> files, parsing to get just id and title. Is there any other data source
>> Hi Neeti,
>> this is a non bioperl way to download the data.
>> Use the SRS server on the EBI page to download only id and title lines
>> from
>> pdb.
>> 1) Point your browser to the SRS page (http://srs.ebi.ac.uk).
>> 2) Search for 'PDB' on the 'library page' and select it.
>> 3) Use the standard query form. Select 'id' in the dropdown list and
>> insert '*' (wildcard).
>> 4) Create a view by selecting 'ID' and 'Title', then click the search
>> button.
>> 5) Click the save results button.
>> 6) Select 'file' in the 'output to' area and 'ALL' in the 'Number of
>> entries
>> to download' field. Press 'save'.
>> If the download is slow, read the 'download tips' on the download page and
>> split the results in chunks.
>> --
>> Oliver
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Bernd Mueller
phone: +49 179 2336692
email: bernd at kirx.de

More information about the Bioperl-l mailing list