Subject: Searching the PDB for general Sequences, etc.

From: <[email-masked]>
Date: Wed, 12 Apr 95 11:50:59 -0500

> Jeff Nauss writes:
>
> I want to search the PDB for structures that have the tripeptide
> sequence Asn-X-Glu where X is any amino acid.  The purpose of the
> search is to identify possible structural motifs for the sequence
> within proteins.  Thus far, I have not found how to do this using the
> Brookhaven search engines on the WWW.  Does any one have a way to
> perform this search?
>
> Alternatively, I could search sequence databases such as SWISS-Prot
> and then cross-reference the hits with the PDB.  However, I have yet
> to find a way to perform the search using wildcards.
>
> Any suggestions?

     Check out the SLEUTH software written in my group. It was designed
 to do just that sort of thing. It lets you search a database compiled
 from the current PDB structures for generalized sequence, phi-psi-chi
 angle ranges, solvent accessibility, secondary structure type, ranges
 of interresidue distances, etc.

 Get the package via anon.ftp or WWW from dasher.wustl.edu (128.252.162.151).

                               Jay Ponder
                               Asst. Prof., Biochemistry
                               Washington Univ. Med. School, St. Louis
                               email:  [email-masked]