Re: CCL:Searching for sequences
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.
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