Subject: Re: CCL-Searching for sequen

From: "Don Gregory" <[email-masked]>
Date: 12 Apr 1995 13:35:12 +0000

Reply to:   RE>CCL:Searching for sequences
On 4/12; Jeff Nauss wrote:
=================
"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?

Thanks in advance...
						Jeff Nauss"
==================
Jeff, This is a capability that Quanta has had for quite some time
in it's Protein Design toolset.  In addition, one can request that
the peptide also have a specified secondary structure type,
and/or specific phi,psi angles.
I did a quick search on a small subset database of the pdb that
we use for demos (only 40 proteins recommended for using as
a homology construction reference set), and I got the following
results, superimposed around the backbone of the "x" residue:
(Note, I only list the central residue, as they are all asn-x-glu)

Protein         res. no.            middle res.
3app                13                     asp
1f19              L:77                    leu
1f19              L:164                   thr
5cha              A:18                     gly
(note that the 5cha has a B chain of the same sequence)

This can also be done on the whole of the pdb, which we have as
well, but I only searched our demo subset.  Hope this helps a bit.
Don Gregory
Mgr. Life Science Applications
MSI