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
