[BiO BB] information on domains

Dan Bolser dan.bolser at gmail.com
Tue Feb 9 07:23:00 EST 2010

On 5 February 2010 05:04, gurunath katagi <gurukatagi at gmail.com> wrote:
> Dear all,
> I wanted to make a dataset of proteins with single domains .
> I wanted to know is there any way that i can get the info. on no. of
> structural domains given a PDB ID or scop id ? (set of PDB ids)
> I tried both with PDB and SCOP and i was not successful ?
> Can any body help me regarding this ?

Hi Gurunath,

I made a list of single domain proteins for my Ph. D research. I did
this by combining the SCOP flat files [1] with the PDB's and MSD's
'biounit' information [2]. I then validated a fraction of them
(biounits are notoriously difficult to predict computationally) by
checking Pisa [3] and the literature.

I'll find where that list is lurking and make it public on PDBWiki [4].

In the mean time, I'd suggest emailing the pdb-l mailing list [5], as
I'm sure their will be lots of people there who can help too.
Previously I was maintaining a list of 'mailing lists for biologists',
but unfortunately that site is down at the moment.


[1] http://scop.mrc-lmb.cam.ac.uk/scop/parse/index.html
[2] http://www.pdbwiki.org/index.php/Biological_unit
[3] http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
[4] http://www.pdbwiki.org
[5] https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l

> Thank you
> Gurunath
> --
> Gurunath M Katagi
> Graduate Research Student
> Bio molecular computation Laboratory
> Supercomputer Education & Research Center
> Indian Institute Of Science, Bangalore- 560012
> Karnataka State, India
> Phone:080-22932737-319,080-22933061
> email: gurunath at rishi.serc.iisc.ernet.in
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bbb

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