From chemistry-request@ccl.net Fri Jul 4 08:50:47 2003 Received: from guppy.vub.ac.be (dekrant.vub.ac.be [134.184.129.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h64Cokqe029776 for ; Fri, 4 Jul 2003 08:50:47 -0400 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id OAA11475; Fri, 4 Jul 2003 14:50:46 +0200 (MET DST) for From: cbiot|at|ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id OAA19626; Fri, 4 Jul 2003 14:50:45 +0200 (MET DST) for Message-ID: <3F0593D8.6090709|at|ulb.ac.be> Date: Fri, 04 Jul 2003 14:48:56 +0000 Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: fr, en-us MIME-Version: 1.0 To: Liste CCL Subject: units Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear folks, When generating the electrostatic potential surface with Molekel (http://www.cscs.ch/molekel/), what are the units? I guess eV, but I am not sure! best regards Christophe From chemistry-request@ccl.net Fri Jul 4 06:56:49 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h64Aunqe027718 for ; Fri, 4 Jul 2003 06:56:49 -0400 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h64AuYka042915 for ; Fri, 4 Jul 2003 12:56:35 +0200 (CEST) Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id h64AuUnE093462; Fri, 4 Jul 2003 12:56:30 +0200 (MEST) Date: Fri, 4 Jul 2003 12:56:30 +0200 (MEST) From: Michel Petitjean Message-Id: <200307041056.h64AuUnE093462)at(ds10.itodys.jussieu.fr> To: chemistry)at(ccl.net Subject: call for papers / 2nd announcement X-Antivirus: scanned by sophie at shiva.jussieu.fr To: chemistry)at(ccl.net Subj: call for papers / 2nd announcement Dear CCL netters, ENTROPY is an electronic journal free for readers. Special issues are planned: see the website of the journal at http://www.mdpi.org/entropy More specifically, a special issue about: "Symmetry, Asymmetry and Similarity" is planned to appear in december (deadline: october 1st) Manuscripts are welcome. Instructions for authors: http://www.mdpi.org/entropy Libraries cannot subscribe to all journals. Publishing in an electronic journal free for readers ensures that papers are available for a wide community. Michel Petitjean, Guest Editor of Entropy, Email: petitjean)at(itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean)at(ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html From chemistry-request@ccl.net Fri Jul 4 04:16:54 2003 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 h648Gqqe022977 for ; Fri, 4 Jul 2003 04:16:53 -0400 Received: from [157.193.201.230] (unknown [157.193.201.230]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 39F216815F for ; Fri, 4 Jul 2003 10:16:10 +0200 (CEST) Subject: AutoDock and protein-protein interactions From: Dominique Vlieghe To: forum CCL Content-Type: text/plain Organization: Message-Id: <1057306539.12980.2.camel$at$dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 04 Jul 2003 10:15:39 +0200 Content-Transfer-Encoding: 7bit Hello all, * A general question: I was wondering whether AutoDock is suitable for studying protein-protein interactions. In principle it is, but speed is the practical limitation I presume. Does anyone have experience with this? * a more specific question: A way of circumventing a huge grid would be to use a smaller grid (assuming that the interacting residues must be 'close' to the receptor) and setting the extnrg parameters to 0.0 kcal mol-1 (meaning that atoms outside the grid would feel no field). Is this a correct assumption? Would this speed up the calculations? Furthermore, are there other ways of avoiding the calculation of interactions involving ligand atoms that are too far away from the receptor? This would make sense, because in P-P interaction only a 'small' number of residues normally contribute to the interaction. Are they any ways of doing this in AutoDock? Regards, Dominique P.S. What happened to the autodock mailing list? -- ------------------------------ 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)9-33-13.692 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe$at$dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------