From chemistry-request@ccl.net Thu Mar 18 05:52:28 2004 Received: from eos.fwall.u-szeged.hu (eos.fwall.u-szeged.hu [160.114.120.248]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2IAqRjs013369 for ; Thu, 18 Mar 2004 05:52:28 -0500 Received: from localhost ([127.0.0.1] helo=eos.fwall.u-szeged.hu) by eos.fwall.u-szeged.hu with smtp (Exim 4.24) id 1B3vAr-0003xn-G7 for chemistry/at/ccl.net; Thu, 18 Mar 2004 11:54:53 +0100 Received: from eos.fwall.u-szeged.hu ([127.0.0.1]) by eos.fwall.u-szeged.hu (SAVSMTP 3.0.0.44) with SMTP id M2004031811545315993 for ; Thu, 18 Mar 2004 11:54:53 +0100 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by eos.fwall.u-szeged.hu with esmtp (Exim 4.30) id 1B3vAn-0003xj-MX for chemistry/at/ccl.net; Thu, 18 Mar 2004 11:54:53 +0100 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr/at/ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id LAA30079 for ; Thu, 18 Mar 2004 11:54:49 +0100 Received: (qmail 15397 invoked by uid 525); 18 Mar 2004 10:54:49 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 18 Mar 2004 10:54:49 -0000 Date: Thu, 18 Mar 2004 11:54:49 +0100 (CET) From: "Dr. Csaba Hetenyi" To: Xavier Gallet cc: chemistry/at/ccl.net Subject: Re: CCL:energy of interaction In-Reply-To: <2092.213.56.212.58.1079537751.squirrel/at/webmail.genodyssee.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-SZTE-local: YES X-SZTE-AVcheck: YES X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, There is a nice collection of protein-protein scoring formulae in Protein Engng. 15(8) 677-681, 2002. Hope, it helps. Best wishes, Csaba On Wed, 17 Mar 2004, Xavier Gallet wrote: > Dear CCLers, > > I'm testing a protein-protein docking program with one receptor molecule > and several potential ligands. My main filter to remove false-positive > solutions concerns mutagenesis data involving several residues both on the > receptor and on the ligands. But I'd like to have a view of the energy of > interaction for the solutions I selected. Do you know a program that could > provide such empirical energy values ? > Thank you in advance. > > Yours sincerely, > > Xavier Gallet > Bioinformatics and IT > GenOdyssee SA > www.genodyssee.com > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY/at/ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > ------ Csaba Hetenyi, MSc, PhD Dept. of Medical Chemistry, University of Szeged, 8 Dom ter, Szeged 6720, Hungary From chemistry-request@ccl.net Thu Mar 18 04:39:10 2004 Received: from atc.atccu.chula.ac.th (atc.atccu.chula.ac.th [192.207.64.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2I9d6js010691 for ; Thu, 18 Mar 2004 04:39:07 -0500 Received: (from nobody@localhost) by atc.atccu.chula.ac.th (8.9.3/8.9.3) id RAA12222; Thu, 18 Mar 2004 17:06:31 +0700 Date: Thu, 18 Mar 2004 17:06:31 +0700 Message-Id: <200403181006.RAA12222$at$atc.atccu.chula.ac.th> From: "Nadtanet Nunthaboot" To: chemistry$at$ccl.net Subject: superimpose small molecule program X-Mailer: NeoMail 1.25 X-IPAddress: 131.130.44.211 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net -- NeoMail - Webmail that doesn't suck... as much. http://neomail.sourceforge.net Dear CClers, I want to superimpose and alignment small molecules. Anybody known about program for superimpose or alignment small molecules? Please tellme about this information.I will appreciate for your help. Thanks a lot. Best Wishes, Nadtanet From chemistry-request@ccl.net Thu Mar 18 11:54:16 2004 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 i2IGsFjs029141 for ; Thu, 18 Mar 2004 11:54:15 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.10/jtpda-5.4) with ESMTP id i2IGuiRb023503 for ; Thu, 18 Mar 2004 17:56:44 +0100 (CET) X-Ids: 168 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id i2IGueeP293380; Thu, 18 Mar 2004 17:56:40 +0100 (MET) Date: Thu, 18 Mar 2004 17:56:40 +0100 (MET) From: Michel Petitjean Message-Id: <200403181656.i2IGueeP293380/at/ds10.itodys.jussieu.fr> To: chemistry/at/ccl.net Subject: CCL:Re: superimpose small molecule program X-Miltered: at shiva.jussieu.fr with ID 4059D4CC.000 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry/at/ccl.net Subject: CCL:superimpose small molecule program Look to the freeware CSR. Program, documentation, refernces: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR Michel Petitjean, Email: petitjean/at/itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean/at/ccr.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html ............................................................... "Nadtanet Nunthaboot" wrote: >Dear CClers, > >I want to superimpose and alignment small molecules. Anybody known >about program for superimpose or alignment small molecules? Please >tellme about this information.I will appreciate for your help. Thanks >a lot. > >Best Wishes, >Nadtanet From chemistry-request@ccl.net Thu Mar 18 16:58:07 2004 Received: from hermes1.cf.ac.uk (hermes1.cf.ac.uk [131.251.0.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2ILw6js007751 for ; Thu, 18 Mar 2004 16:58:06 -0500 Received: from maincf1p.cf.ac.uk ([131.251.4.20]) by hermes1.cf.ac.uk with esmtp (Exim 4.24) id 1B45Z6-0002rJ-Dk for CHEMISTRY_at_ccl.net; Thu, 18 Mar 2004 22:00:36 +0000 Received: from Cardiff_University-MTA by MAINCF1P.cf.ac.uk with Novell_GroupWise; Thu, 18 Mar 2004 22:00:36 +0000 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.1 Date: Thu, 18 Mar 2004 22:00:42 +0000 From: "Dimitrios Vlachakis" To: Subject: CCL:superimpose small molecule program Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Nadtanet, try the swiss pdb viewer (freeware) from http://au.expasy.org/spdbv/ you can do multi-alignments, superimpose and evaluate superimposition by RMSd by: -CA -backbone -sidechain -or full structure cheers... Dimitrios Vlachakis PhD student in Molecular Modelling Medicinal Chemistry Group Welsh School of Pharmacy Cardiff University Redwood Building King Edward VII Avenue CF10 3XF Cardiff Wales, UK tel. +44 2920 877221 tel. +44 2920 874551 (lab) fax. +44 2920 874537 ................................................................................... From chemistry-request@ccl.net Thu Mar 18 15:12:24 2004 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2IKCNjs005226 for ; Thu, 18 Mar 2004 15:12:23 -0500 Received: from nyssa.bchs.uh.edu (Nyssa.BCHS.UH.EDU [129.7.238.204]) by Post-Office.UH.EDU (PMDF V6.0-025 #30599) with ESMTP id <0HUS04JIBG761B:at:Post-Office.UH.EDU> for chemistry:at:ccl.net; Thu, 18 Mar 2004 14:13:54 -0600 (CST) Date: Thu, 18 Mar 2004 14:14:37 -0600 From: Jerry Ebalunode Subject: purchasing or acquiring nci compounds To: ccl Reply-to: jebalunode:at:UH.EDU Message-id: <200403181414.37395.jebalunode:at:uh.edu> Organization: University of Houston MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Content-disposition: inline User-Agent: KMail/1.6.1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi all, Where can check for the availabilty and possibly purchase of certain compounds from the NCI database of organic compounds? -- Cheers, Jerry Ebalunode Graduate Research Assistant RM 402F Houston Science Center Phone: 713-743-8367 Dept. of Biology and Biochemistry University of Houston. 4800 Calhoun Road Houston, TX 77204 From chemistry-request@ccl.net Thu Mar 18 12:26:58 2004 Received: from fornells.imim.es (fornells.imim.es [193.147.240.141]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i2IHQvjs030951 for ; Thu, 18 Mar 2004 12:26:57 -0500 Received: by fornells.imim.es with Internet Mail Service (5.5.2657.72) id ; Thu, 18 Mar 2004 18:28:20 +0100 Received: from imim.es (diana.imim.es [193.146.190.154]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2657.72) id HDQFZ23B; Thu, 18 Mar 2004 18:27:07 +0100 From: "Barbany, Montse" To: chemistry/at/ccl.net Message-ID: <4059DD93.4020404/at/imim.es> Date: Thu, 18 Mar 2004 18:34:11 +0100 User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 Subject: CCL:superimpose small molecule program] Content-Type: multipart/alternative; boundary="------------090500030109040600090801" X-Spam-Status: No, hits=1.0 required=7.0 tests=HTML_20_30,HTML_MESSAGE, HTML_TITLE_EMPTY autolearn=no version=2.61 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------090500030109040600090801 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Michel, I am the developer of program MIPSim, a program that performs an automatic alignment of small molecules based on molecular interacion potentials. You can download it on http://diana.imim.es/software/mipsim/index.html It is free for academics. Best wishes Montse "Nadtanet Nunthaboot" wrote: >Dear CClers, > >I want to superimpose and alignment small molecules. Anybody known >about program for superimpose or alignment small molecules? Please >tellme about this information.I will appreciate for your help. Thanks >a lot. > >Best Wishes, >Nadtanet -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow/at/nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Montserrat Barbany Puig Computational Structural Biology Laboratory Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Pg.Marmtim de la Barceloneta, 37-49; 08003 Barcelona (Spain) Tel: +34 93 224 0893 // +34 93 224 0875 e-mail: mbarbany/at/imim.es http://www.imim.es/grib/ --------------090500030109040600090801 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 
Dear Michel,

I am the developer of program MIPSim, a program that performs an automatic alignment of small molecules based on molecular
interacion potentials. 
You can download it on 
http://diana.imim.es/software/mipsim/index.html

It is free for academics.

Best wishes

Montse






"Nadtanet Nunthaboot"  wrote:
>Dear CClers,
>
>I want to superimpose  and alignment small molecules. Anybody known 
>about program for superimpose or alignment small molecules?  Please 
>tellme about this information.I will appreciate for your help. Thanks 
>a lot.
>
>Best Wishes,
>Nadtanet

-= This is automatically added to each message by the mailing script =-
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-- 
Montserrat Barbany Puig

Computational Structural Biology Laboratory
Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
Pg.Marítim de la Barceloneta, 37-49; 08003 Barcelona (Spain)
Tel: +34 93 224 0893 // +34 93 224 0875
e-mail: mbarbany/at/imim.es         http://www.imim.es/grib/
--------------090500030109040600090801--