From chemistry-request@ccl.net Tue Dec 30 07:02:15 2003 Received: from elrond.chem.uni.wroc.pl (elrond.chem.uni.wroc.pl [156.17.103.206]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBUC1hTC024501 for ; Tue, 30 Dec 2003 07:01:43 -0500 Received: from jarek (helo=localhost) by elrond.chem.uni.wroc.pl with local-esmtp (Exim 3.35 #1 (Debian)) id 1AbIZB-0001ev-00 for ; Tue, 30 Dec 2003 13:01:41 +0100 Date: Tue, 30 Dec 2003 13:01:41 +0100 (CET) From: Jaroslaw Panek To: chemistry_at_ccl.net Subject: CCL: when to take a logarithm of biological activity in QSAR studies? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, there is an established tradition of taking a LOGARITHM of concentrations (e.g. -log (IC50), -log(ED50) ) as biological activity parameter in QSAR studies. As I understand, this comes either from the need to bring widely different numerical data (like 0.0001 and 0.1) into more balanced scale, or from generally logarithmic nature of biological response to external stimuli. Now, my question is: do you think that when applying other, non-concetration-based types of biological activity, one should also take their logarithm for QSAR studies? I am thinking specifically about percentages, as in "inhibition percentage", which are commonly encountered as results of biological assays. Happy New Year to everybody! Jaroslaw Panek Faculty of Chemistry, University of Wroclaw ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland From chemistry-request@ccl.net Tue Dec 30 03:49:44 2003 Received: from mail1.cc.huji.ac.il (mail1.cc.huji.ac.il [132.64.1.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBU8nCTC021852 for >ccl.net>; Tue, 30 Dec 2003 03:49:13 -0500 Received: by mail1.cc.huji.ac.il (Postfix, from userid 31998) id 0D00E4000B; Tue, 30 Dec 2003 10:49:05 +0200 (IST) Received: from webmail.cc.huji.ac.il (webmail.cc.huji.ac.il [132.64.1.3]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id 6235640009 for >ccl.net>; Tue, 30 Dec 2003 10:49:05 +0200 (IST) Received: (from nobody@localhost) by webmail.cc.huji.ac.il (8.11.6/8.11.6) id hBU8n5611831 for CHEMISTRY<>ccl.net; Tue, 30 Dec 2003 10:49:05 +0200 Received: from angeles-4.ch.huji.ac.il (angeles-4.ch.huji.ac.il [132.64.90.90]) by webmail.huji.ac.il (IMP) with HTTP for >chem.ch.huji.ac.il>; Tue, 30 Dec 2003 10:49:05 +0200 X-Authentication-Warning: webmail.cc.huji.ac.il: nobody set sender to avitals<>chem.ch.huji.ac.il using -f Message-ID: <1072774145.3ff13c01e68d7<>webmail.huji.ac.il> Date: Tue, 30 Dec 2003 10:49:05 +0200 From: avitals<>chem.ch.huji.ac.il To: CHEMISTRY<>ccl.net Subject: localized orbitals continued MIME-Version: 1.0 Content-Type: text/plain; charset=windows-1255 User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Originating-IP: 132.64.90.90 X-Spam-Level: X-Spam-Status: No, hits=0.1 required=7.0 tests=NO_REAL_NAME,USER_AGENT_IMP,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hBU8niTC021862 Hi, I tried using gOpenMol, Molden, Molekel, ArgusLab and Gaussview in order to draw LOCALIZED orbitals. All of these programs are great for drawing MOLECULAR orbitals, but how can I draw localized atomic orbitals, and view the hybridization? Thanks, Avital ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/ From chemistry-request@ccl.net Tue Dec 30 08:41:30 2003 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hBUDevTC026182 for ; Tue, 30 Dec 2003 08:40:57 -0500 Received: from cosmologic.de (xdsl-213-196-217-119.netcologne.de [213.196.217.119]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id ACK29508 (AUTH klamt{at}cosmologic.de); Tue, 30 Dec 2003 14:40:08 +0100 (CET) Message-ID: <3FF18033.8080502{at}cosmologic.de> Date: Tue, 30 Dec 2003 14:40:03 +0100 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jaroslaw Panek CC: chemistry{at}ccl.net Subject: Re: CCL:when to take a logarithm of biological activity in QSAR studies? References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,REFERENCES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Jaroslaw, since in physical and biological chemistry we are almost always dealing with "activities" which are portions of compounds being in one state and other portions being in another state, and since the distribution between such states is governed by Boltzmann factors, it is most useful to convert the partition quantities to free energy quantities by taking the logarithm. All of our molecular QSAR descriptors are much more likely to be linearly related to the free energies than to the original partition properties. For the same reason I also recommend to convert biological activities as binding percentages or percentage of intestinal absorption into logarithmic partition properties. But care has to be taken since you have to do it in the following way: Let PA be the percentage being in the specified state A. Then we have a percentage PnonA = 100 - PA not being in state A and the logarithmic distribution between state A and nonA is log(PA/(100-PA)) Furthermore, typically data measured or collected on a percentage scale are quite crude at the ends, i.e. close to 0 and 100, while the logarithmic scale is quite sensitive there. So you should exclude measurements too close to 0 or 100 from the QSAR regression and may finally confirm whether you generated model correctly predicts the activities of the respective compounds close eneough to 0 or 100. Regards Andreas Jaroslaw Panek wrote: >Dear CCLers, > >there is an established tradition of taking a LOGARITHM of concentrations >(e.g. -log (IC50), -log(ED50) ) as biological activity parameter in QSAR >studies. As I understand, this comes either from the need to bring widely >different numerical data (like 0.0001 and 0.1) into more balanced scale, >or from generally logarithmic nature of biological response to external >stimuli. Now, my question is: do you think that when applying other, >non-concetration-based types of biological activity, one should also take >their logarithm for QSAR studies? I am thinking specifically about >percentages, as in "inhibition percentage", which are commonly encountered >as results of biological assays. > >Happy New Year to everybody! > >Jaroslaw Panek >Faculty of Chemistry, University of Wroclaw >ul. F. Joliot-Curie 14, 50-383 Wroclaw, Poland > > > >-= 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, jkl{at}ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt{at}cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics --------------------------------------------------------------------------------