From sunger@crl.com Mon Apr 17 18:45:49 1995 Received: from mail.crl.com for sunger@crl.com by www.ccl.net (8.6.10/930601.1506) id SAA23813; Mon, 17 Apr 1995 18:44:13 -0400 Received: from crl6.crl.com by mail.crl.com with SMTP id AA22430 (5.65c/IDA-1.5 for ); Mon, 17 Apr 1995 15:43:35 -0700 Received: by crl6.crl.com id AA25054 (5.65c/IDA-1.5); Mon, 17 Apr 1995 15:42:31 -0700 Date: Mon, 17 Apr 1995 15:42:30 -0700 (PDT) From: Stefan Unger To: "Jeffrey L. Nauss" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:Searching for sequences In-Reply-To: <9504121351.AA22866@ucmod2.che.uc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Protein Expert (for MAC and PowerMAC) will do this. You create a folder with whatever PDB files you want and it will then create a database of sequence, contact distance and phi/psi angles. You can then construct searches with up to five "positions". Each position can be an ambiguous sequence (e.g. "lipophilic"), or specific amino acid, distance or angle relationship. The hits are shown visually and data can also be output to, say, Excel. I am the distributor. Please contact me directly if you would like further information. BioSoftware Marketing 4151 Middlefield Rd., Ste 109 Palo Alto, Ca 94303-4743 415-858-0522 fx: 415-858-0521 On Wed, 12 Apr 1995, 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 > > **************************************************************************** > * UU UU Jeffrey L. Nauss, PhD * > * UU UU Director, Molecular Modeling Services * > * UU UU Department of Chemistry * > * UU UU CCCCCCC University of Cincinnati * > * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * > * UUUU CC * > * CC Telephone: 513-556-0148 Fax: 513-556-9239 * > * CC * > * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * > * CCCCCCC http://www.che.uc.edu/~nauss * > **************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: nauss@ucmod2.che.uc.EDU > -- Original Sender From: Address: nauss@ucmod2.che.uc.EDU > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > >