From chemistry-request@ccl.net Tue Jan 20 10:41:28 2004 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0KFfRc1022494 for ; Tue, 20 Jan 2004 10:41:28 -0500 Received: from dmbr032.fvms.ugent.be (dmbr032.fvms.ugent.be [157.193.200.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id CE1FF80010 for ; Tue, 20 Jan 2004 16:42:25 +0100 (CET) Subject: Energetical evaluation of protein-protein interactions From: Dominique Vlieghe To: forum CCL Content-Type: text/plain Organization: Message-Id: <1074613380.21437.4.camel!at!dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 20 Jan 2004 16:43:00 +0100 Content-Transfer-Encoding: 7bit Hi all, Does anyone know of a good protocol for evaluating the energetics of protein-protein interactions? More precisely, I would like to evaluate the individual residue-residue contributions in complex stabilisation. Also, does anyone have experience in doing this using CHARMM? Regards (and a late happy new year :-0 ) Dominique -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University (new) 'Fiers-Schell-Van Montagu' building (new) Technologiepark 927 (new) B-9052 Ghent (Zwijnaarde), Belgium (new) Tel : +32-(0)9-33-13.693 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe!at!dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------ From chemistry-request@ccl.net Tue Jan 20 03:57:42 2004 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0K8vfc1003842 for ; Tue, 20 Jan 2004 03:57:41 -0500 Received: from uni-koeln.de (relax.cubic.Uni-Koeln.DE [134.95.151.118]) by mail1.rrz.Uni-Koeln.DE (8.12.10/8.12.10) with ESMTP id i0K8wcqR027631 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT); Tue, 20 Jan 2004 09:58:41 +0100 (MET) Message-ID: <400CEDBE.9010404..at..uni-koeln.de> Date: Tue, 20 Jan 2004 09:58:38 +0100 From: Christoph Steinbeck Reply-To: c.steinbeck..at..uni-koeln.de Organization: Cologne University Bioinformatics Center User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Joel.Freyss..at..Actelion.Com CC: chemistry..at..ccl.net, raj kumar Subject: Re: CCL:MM2 ForceField in Java References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Joel, we are doing exactly the same at the moment, as part of our student education. Unfortunately, we are at the same point like you, so it seems we duplicated some work. Our MM2 implementation is based on the MM2 parameter set from the Tinker package. I would be delighted to exchange some thoughts or the source code. My group, embedded in an international team of developers, maintains and develops the Chemistry Development Kit (CDK) [1], http://cdk.sourceforge.net. This new MM2 implementation will be part of CDK very soon. Cheers, Chris [1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E. The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 2003, 43, 493-500. -- Dr. rer. nat. habil. Christoph Steinbeck (c.steinbeck..at..uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. Joel.Freyss..at..Actelion.Com wrote: > Hello, > > I am trying to implement a MM2 forcefield in Java. > I found Tinker to be a great help for that work but I wondered if anybody > ever tried to develop something like that in Java and has some hints or > resources to help me? I need to find a position close to a global minimum > in a very short amount of time and the forcefield needs to be reliable. > > Right now, I implemented the bond stretching, angle bending, torsion and > VDW parameters and I get approximative results in about 2s: CH bonds with a > length of 1.05 A, using the simulated annealing and then the steepest > descent algorithm. > > Any advise? > Thanks > > Joel From chemistry-request@ccl.net Tue Jan 20 16:19:31 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0KLJRc1002500 for >ccl.net>; Tue, 20 Jan 2004 16:19:31 -0500 Received: from 128.195.173.206 (dhcp-173206.mobile.uci.edu [128.195.173.206]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i0KLKHqO026448 for >ccl.net>; Tue, 20 Jan 2004 13:20:22 -0800 Date: Tue, 20 Jan 2004 13:20:17 -0800 From: John Lee >joyie.com> X-Mailer: The Bat! (v1.62r) Reply-To: John Lee >joyie.com> X-Priority: 3 (Normal) Message-ID: <1465005816.20040120132017<>joyie.com> To: chemistry<>ccl.net Subject: The difference between partial optimization(Z-matrix) and freeze the coordinates(modredundant) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found Dear CCLers, In the partial optimization, we can use Z-matrix and specify Variables and Constants to do partially optimization. There is also another way to do this kind of "partial optimization" which is to use modredundant to freeze the position of an atom, bond, angle and dihedral angle. Except fixing the position of an atom, it seems I can perform partial optimization with Z-matrix for bond, angle and dihedral angle instead of using modredundant to freeze them. So I wander what is the differences between them. -- Best regards, John From chemistry-request@ccl.net Tue Jan 20 18:31:16 2004 Received: from genscript.com ([209.19.21.18]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i0KNVEc1008551 for ; Tue, 20 Jan 2004 18:31:15 -0500 Message-Id: <200401202331.i0KNVEc1008551(at)server.ccl.net> Received: (qmail 27391 invoked from network); 21 Jan 2004 02:18:18 -0000 Received: from unknown (HELO localhost) (192.168.1.103) by 0 with SMTP; 21 Jan 2004 02:18:18 -0000 Mime-version: 1.0 Content-type: text/plain; charset="iso-8859-1" Date: Tue, 20 Jan 2004 18:18 -0800 Subject: Boost Protein Expression by Codon Optimization To: chemistry(at)ccl.net From: Sally Wang Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i0KNVGc1008565 Dear Colleague, Happy New Year! As we know, codon preference among different species could be dramatically different. 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