From chemistry-request@server.ccl.net Sun Jul 16 04:50:57 2000 Received: from mailgate.dfh.dk (web-cache.dfh.dk [130.225.176.26]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA08673 for ; Sun, 16 Jul 2000 04:50:51 -0400 Received: from f-lhk.dfh.dk (dhcp225-220.dfh.dk [130.225.225.220]) by mailgate.dfh.dk (8.9.3/8.9.3) with SMTP id KAA12411; Sun, 16 Jul 2000 10:52:11 +0200 Message-Id: <3.0.6.32.20000716105029.0079ab10@compchem.dfh.dk> X-Sender: anne@compchem.dfh.dk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Sun, 16 Jul 2000 10:50:29 +0200 To: anne@compchem1.dfh.dk From: Anne Subject: CCL:protein folding/sequence. Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA08674 Homology does not mean "amino acid sequence similarity >20%" It is defined in terms of functionality (cf. analogy). For a clear definition see Attwood, T. K. & Parry-Smith, D. J. (1999). Introduction to bioinfomatics (Cell and Molecular biology Series), Addison Wesley Longman Ltd., Harlow, England. Comparative modelling methods require more than aligning protein sequences, constructing structural models against canonical quaternary, tertiary and secondary structural element templates or using threading methodologies and then minimisation. It is increasingly knowledge based, requiring more information on protein domain motions (normal mode analysis), catalytic group analysis, protein-protein activation and modification, expression and regulation. For seminal papers perform citation searches on the following publications and look for reviews that have used or criticised: Chou & Fasman (1978). Advances in Enzymology, 47, 45-148 Godzik et al (1993). J Computer-aided molecular design, 7, 397-438 Jones et al (1992). Nature 358, 86-89 Luthy et al (1992). Nature 356, 83-85 Mosimann et al (1995). Proteins 23, 301-317 Novotny et al (1988). Proteins 4, 19-30 good luck James Smith > I hear that if two sequences have homology (biological sequence > similarity) > greater than 20%, then their 3-d structures will be almost identical. > > Is this true? If so, can someone point me to some seminal papers > discussing > this... > > Thanks in advance. I will summarize if enough interest is shown. > > Best Wishes, Iraj. > _________________________________________________________________________ James Smith The Drug Design Group 01123 331 987 (Office) St.John's College Department of Pharmacology 01223 331 740 (Fax) Cambridge University of Cambridge 07625 395 084 (Pager) CB2 1TP CB2 1QJ js252@cam.ac.uk United Kingdom United Kingdom http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Sun Jul 16 12:23:59 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA11121 for ; Sun, 16 Jul 2000 12:23:58 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id SAA08859 for ; Sun, 16 Jul 2000 18:48:11 +0200 (CEST) Date: Sun, 16 Jul 2000 18:48:11 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: AutoDock 3 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl'ers, lately I experienced a problem after I prepared input files for AutoDock 3. The program terminates after it read the dpf-file with the following message: autodock3: NOW IN COMMAND MODE. I don't really understand this, because I prepared the input files in the same manner as I have done it several times before. Any help is appreciated. Best regards, Christian ----------------------------------------------------------------- Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de -----------------------------------------------------------------