From chemistry-request@server.ccl.net Tue Apr 16 00:45:50 2002 Received: from herodot ([195.41.198.113]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3G4joj15513 for ; Tue, 16 Apr 2002 00:45:50 -0400 Received: from localhost.localdomain (cpe.atm0-0-0-145140.0xc2c0875d.boanxx3.customer.tele.dk [194.192.135.93]) by herodot (Postfix) with ESMTP id E569017ACD for ; Tue, 16 Apr 2002 06:45:39 +0200 (CEST) Subject: Re: CCL:gear iterators From: Kenneth Geisshirt To: chemistry@ccl.net In-Reply-To: <000a01c1e4b5$faa7f7d0$2e30e980@wardgroup> References: <000a01c1e4b5$faa7f7d0$2e30e980@wardgroup> Content-Type: text/plain; charset=ISO-8859-1 X-Mailer: Ximian Evolution 1.0.3 Date: 16 Apr 2002 06:45:39 +0200 Message-Id: <1018932340.454.26.camel@homer> Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g3G4joj15514 On Mon, 2002-04-15 at 21:44, H. Martin Gillis wrote: > If anyone knows where I can obtain software of GEAR Iterators (prefereably freeware) it will be most appreciated. GNU Scientific Library implements a number of ODE solvers. Check out http://sources.redhat.com/gsl/ -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 From chemistry-request@server.ccl.net Tue Apr 16 00:50:34 2002 Received: from donkeykong.gpcc.itd.umich.edu (smtp@[141.211.2.163]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3G4oYj15587 for ; Tue, 16 Apr 2002 00:50:34 -0400 Received: from amidar.gpcc.itd.umich.edu (amidar.gpcc.itd.umich.edu [141.211.2.209]) by donkeykong.gpcc.itd.umich.edu (8.8.8/4.3-mailhub) with ESMTP id AAA07823; Tue, 16 Apr 2002 00:50:24 -0400 (EDT) Received: from localhost (brupalf@localhost) by amidar.gpcc.itd.umich.edu (8.9.1a/5.1-client) with ESMTP id AAA01055; Tue, 16 Apr 2002 00:50:24 -0400 (EDT) Precedence: first-class Date: Tue, 16 Apr 2002 00:50:24 -0400 (EDT) From: Bruce Allan Palfey X-X-Sender: brupalf@amidar.gpcc.itd.umich.edu To: "H. Martin Gillis" cc: chemistry@ccl.net, Subject: Re: CCL:gear iterators In-Reply-To: <000a01c1e4b5$faa7f7d0$2e30e980@wardgroup> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Marcelo There are anumber of programs (including free programs) that will simulate chemical kinetics. Look under "software" at http://www.med.umich.edu/biochem/enzresources/ KINSIM and its various ports uses the Gear algorithm, which is useful for "stiff" systems; that may not be necessary for your kinetic system. Berkeley Madonna is a very versatile package that includes the Gear algorithm, but it is not free (though the demo is almost fully functional). Rather than solve differential equations, CKS (free from IBM) uses a stochastic approach to simulate reactions, avoiding the pitfalls of stiff systems. There are many others; hope this helps. ciao, Bruce Palfey University of Michigan Department of Biological Chemistry Ann Arbor, MI 48109-0606 On Mon, 15 Apr 2002, H. Martin Gillis wrote: > I want to model reaction rate constants where all four compunds A,B,C > and D are interconvertble and where an equilibrium is eventually > established. > > I have searched the literature and found that the use of an algorythm > known as GEAR iteration will do the job provided that the concentrations > of all 4 components versus time are known. > > If anyone knows where I can obtain software of GEAR Iterators > (prefereably freeware) it will be most appreciated. > > Marcelo Sales > Dept of Chemistry > University of Saskatchewan > sales@duke.usask.ca > > > From chemistry-request@server.ccl.net Tue Apr 16 09:24:08 2002 Received: from aspirine.u-strasbg.fr (IDENT:root@[130.79.84.250]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3GDO7j25292 for ; Tue, 16 Apr 2002 09:24:07 -0400 Received: from hit8.pharma.u-strasbg.fr (lead2.u-strasbg.fr [130.79.85.21]) by aspirine.u-strasbg.fr (8.10.2/8.10.2) with ESMTP id g3GDLDg18207; Tue, 16 Apr 2002 15:21:13 +0200 Message-Id: <5.1.0.14.0.20020416152026.01733bd8@aspirine.u-strasbg.fr> X-Sender: rognan@aspirine.u-strasbg.fr X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 16 Apr 2002 15:24:00 +0200 To: quch0@yahoo.com From: Didier Rognan Subject: docked datasets Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Please find here a dataset of 100 protein-ligand complexes for which we have computed the top 30 docked solutions using Dock, FlexX and Gold. The dataset can be downloaded at the following URL: http://med-chem.u-strasbg.fr/~didier/db/dock_base.html Regards ----------------------------------------------------------------------------------------------- Dr. Didier ROGNAN Directeur de Recherches - CNRS Laboratoire de Pharmacochimie de la Communication Cellulaire UMR 7081 74, route du Rhin, B.P.24 F-67401 Illkirch phone: +33 (0)3 90 24 42 35 fax: +33 (0)3 90 24 43 10 mobile: +33 (0)6 89 56 24 46 email: didier.rognan@pharma.u-strasbg.fr