From Don_Gregory@msi.com Wed Apr 12 13:44:16 1995 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.10/930601.1506) id NAA10772; Wed, 12 Apr 1995 13:39:10 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA20608; Wed, 12 Apr 95 13:36:19 EDT Message-Id: <9504121736.AA20608@msi.com> Date: 12 Apr 1995 13:35:12 +0000 From: "Don Gregory" Subject: Re: CCL-Searching for sequen To: "Comp. Chem. Listserver" 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