Re: CCL:Searching for sequences

[brian - at - bert.chem.wsu.edu (Brian W. Beck)]

 Jeffrey L. 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
 :
 	There is a sequence database version of the PDB structural
 	database called "NRL_3D". I know that the GCG suite of sequence
 	analysis programs includes it, but I imagine it's probably
 	available from other sources as well. I have no idea whether
 	it's commercial or public. Your best bet would be to find someone
 	who has GCG or Intelligenetics and collaborate.
 	-Brian
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