Hi Ed,
What about submitting the uniprot accession number of your
protein to the PDB?. As you know, this will just list the all entries
where your protein sequence is there..
-Vandu murugan..
On 6/23/12, Ed Pozharski <[email protected]> wrote:
> Silly question.
>
> Say I want to find every structure in the PDB with the exact sequence or
> with perhaps 1-2 mutations. I know of two ways of doing this.
>
> 1. Go to NCBI BLAST and run the sequence against the PDB subset. The
> resulting list will have identities listed, so manual parsing is doable
> if there aren't too many hits.
>
> 2. PDB and PDBe both have the search by sequence features. Trouble is
> the default E value seems to be tailored to poor sequence identity
> (which makes sense if you looking for potential MR models). Sure, I can
> reduce the target E value, but it's a little cumbersome and I have no
> idea what the target level should be so that I don't get any 50%
> identical sequences yet not miss single/double mutants.
>
> Wouldn't it be nice if one could use the sequence identity cutoff/query
> coverage instead? Much more comprehensible than the E-value. Is there
> a search engine that does that? Seems like a fairly common need, and
> perhaps I just can't find on PDB website.
>
> Thanks in advance for any suggestions,
>
> Ed.
>
> --
> Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
> Julian, King of Lemurs
>
