Re: Searching for sequences

[tripos!rigel!david' at \`uunet.uu.net (David Mosenkis)]

 Jeff,
   If you have access to Sybyl from Tripos, the "Search Protein
 Database" item
   on the Biopolymer menu supports the kind of query you specified
   (Asn-X-Glu), and provides convenient access to view and analyze the
   resulting 3D fragments and perform more complex searches.  BTW, I did a
   quick search of that pattern on a non-redundant subset of 343 structures
   from the PDB, and got 227 hits.  A quick followup search revealed that 38
   of these 3-residue fragments are fully contained within alpha helices, and
   14 are fully contained within beta strands.
   Let me know if you'd like more information.
 David Mosenkis  (david' at \`tripos.com)
 Tripos, Inc.