Re: CCL-Searching for sequen

["Don Gregory" <Don_Gregory (+ at +) msi.com>]

         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