On 5 February 2010 05:04, gurunath katagi <[email protected]> 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. HTH, Dan. [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: [email protected] > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
