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Date: Wed, 12 Apr 1995 12:49:03 -0500
From: tripos!rigel!david@uunet.uu.net (David Mosenkis)
Message-Id: <199504121749.MAA24669@rigel.tripos>
To: uunet!ucmod2.che.uc.EDU!nauss@uunet.uu.net
Subject: Re: Searching for sequences
Cc: uunet!ccl.net!CHEMISTRY@uunet.uu.net


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@tripos.com)
Tripos, Inc.