From chemistry-request@ccl.net Mon Jun 9 03:42:37 2003 Received: from web15206.mail.bjs.yahoo.com (web15206.mail.bjs.yahoo.com [202.3.77.136]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h597gTkr019543 for ; Mon, 9 Jun 2003 03:42:33 -0400 Message-ID: <20030609074223.93982.qmail=at=web15206.mail.bjs.yahoo.com> Received: from [218.20.254.51] by web15206.mail.bjs.yahoo.com via HTTP; Mon, 09 Jun 2003 15:42:23 CST Date: Mon, 9 Jun 2003 15:42:23 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: van der Waals radii of element -- summary To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I would like to give acknowledgement to Matt Thompson, Jamie Platts, Michel Petitjean, Fabien Fontaine, and Fedor Goumans for their kindly response to my question. Here is my summary: http://www.ccdc.cam.ac.uk/support/csd_doc/volume1/z1c07076.html or http://www.ccdc.cam.ac.uk/support/csd_doc/started/gs-appendix-5.html the data from A. Bondi (1964) "van der Waals Volumes and Radii" J.Phys.Chem. 68, 441-451, are summarized. If the elements you need are not among those data, you could check S. S. Batanov (1999), J. Mol. Structure, 468, 151-159, where theoretical and experimental data are given for almost all elements. or webelements: http://www.webelements.com/webelements/properties/text/definitions/van-der-waals-radius.html Best regards, Jinsong _________________________________________________________ Do You Yahoo!? AwA,MxBgJ@=g5D!0Dc!1JGK-#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/cn_user_profile_study_may2003 From chemistry-request@ccl.net Sun Jun 8 18:41:15 2003 Received: from sungoddess.ccs.yorku.ca (mailrelay.yorku.ca [130.63.236.144]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h58MfEkr016924 for ; Sun, 8 Jun 2003 18:41:14 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungoddess.ccs.yorku.ca (8.12.9/8.12.8) with ESMTP id h58MfE0O029177 for ; Sun, 8 Jun 2003 18:41:14 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id h58MfBs05270 for chemistry-.at.-ccl.net; Sun, 8 Jun 2003 18:41:11 -0400 (EDT) From: Wai-To Chan Message-Id: <200306082241.h58MfBs05270-.at.-curl.gkcl.yorku.ca> Subject: On basis sets for calculating thermochemistry properties To: chemistry-.at.-ccl.net Date: Sun, 8 Jun 2003 18:41:11 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This is an amendment of my previous message. Perhaps the recommendation of the 6-31+G(d,p) as the minimal basis set to use is too strong and not always pragmatic. My experience is that the '+' can improve accuracy significantly for characterization of the potential surface of floppy radical structures. But diffuse functions can also create convergence difficulties. For calculation of the equilibrium structures of more 'usual' type of molecules I think it would be fine to begin with 6-31G(d,p). Wai-To Chan <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<,, I used the xalpha/3-21g method for geometry optimization of LARGE molecules in the past and got some decent results. But sto-3g and 3-21g won't be a good choice for reliable thermochemistry calculation with Hybrid DFT method like B3LYP. Use a basis set at least as large as 6-31+G(d)/6-31+G(d,p). The inclusion of '+' can make a difference. You may refer to J. Phys. Chem. A, (2003) vol 107 pg 1384-1388 by Lynch, Zhao and Truhlar for an assessment of the accuracy of the MPW1PW91/6-31+G(d,p) method. Wai-To Chan >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From chemistry-request@ccl.net Mon Jun 9 05:56:40 2003 Received: from exasp.biogeo.uw.edu.pl (gate.biogeo.uw.edu.pl [212.87.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h599udkr031755 for ; Mon, 9 Jun 2003 05:56:40 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by exasp.biogeo.uw.edu.pl (Postfix) with ESMTP id DBACF15E28 for ; Mon, 9 Jun 2003 11:56:42 +0200 (CEST) Received: by exasp.biogeo.uw.edu.pl (Postfix, from userid 526) id 32DA615E1B; Mon, 9 Jun 2003 11:56:41 +0200 (CEST) Date: Mon, 9 Jun 2003 11:56:41 +0200 From: Grzegorz Bakalarski To: CHEMISTRY!at!ccl.net Subject: CCL: RE: van der Waals radii of element -- summary Message-ID: <20030609095641.GA20482!at!exasp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4i X-Virus-Scanned: by AMaViS snapshot-20020300 >If the elements you need are not among those data, you >could check S. S. Batanov (1999), J. Mol. Structure, >468, 151-159, where theoretical and experimental data >are given for almost all elements. For those who would like to take a look on that paper: The autor is: S.S. Batsanov ^ and the journal is: J. Mol. Structure: TEOCHEM So in full: Batsanov, S.S., J. Mol. Struc. TEOCHEM (1999), vol. 468, iss. 1-2, pg. 151-159 Regards, GB From chemistry-request@ccl.net Mon Jun 9 05:48:16 2003 Received: from web15209.mail.bjs.yahoo.com (web15209.mail.bjs.yahoo.com [202.3.77.139]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h599m7kr030810 for ; Mon, 9 Jun 2003 05:48:12 -0400 Message-ID: <20030609094805.80066.qmail$at$web15209.mail.bjs.yahoo.com> Received: from [218.1.97.34] by web15209.mail.bjs.yahoo.com via HTTP; Mon, 09 Jun 2003 17:48:05 CST Date: Mon, 9 Jun 2003 17:48:05 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: Some questions about CoMFA To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear all, I am a newbie to Tripos's Sybyl, thus I have some questions about CoMFA. Would you like to give me a hand? Thanks in advance! I have more than two hundred compounds that I hope to carry out CoMFA in order to establish a QSAR model. I am going to divide the large data set to two parts, one for training, and the other for validation. The first question is whether the alignment should be done with a whole data set or with two separated data sets (i.e. training and validation data set). The second question is what are the alignment rules. The third question is how to improve the Q2 or r2. Because the data set includes compounds with a diversity of structure, I hope to find a way to distinguish which are the outliers. Thank you very much for your consideration on this matter! Best regards, Jinsong _________________________________________________________ Do You Yahoo!? AwA,MxBgJ@=g5D!0Dc!1JGK-#? http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/cn_user_profile_study_may2003 From chemistry-request@ccl.net Mon Jun 9 04:53:06 2003 Received: from mserv7.dl.ac.uk (mserv7.dl.ac.uk [148.79.80.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h598r5kr025345 for ; Mon, 9 Jun 2003 04:53:06 -0400 X-DL-MFrom: X-DL-Connect: Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv7.dl.ac.uk (8.12.9/8.12.8/[ref postmaster$at$dl.ac.uk]) with ESMTP id h598r0aZ002406 for ; Mon, 9 Jun 2003 09:53:00 +0100 Message-ID: <3EE444EC.7050201$at$dl.ac.uk> Date: Mon, 09 Jun 2003 09:27:25 +0100 From: "Van Dam, HJJ (Huub)" Organization: CCLRC Daresbury Laboratory User-Agent: Mozilla/5.0 (X11; U; OSF1 alpha; en-US; rv:0.9.4.1) Gecko/20020517 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Summary: Accuracy of RPA linear response calculations Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I would like to thank everyone who responded to my question: > I am planning to do some large scale calculations of excitation spectra > in the Random Phase Approximation (RPA). However, before I burn vast > amounts of CPU cycles I would like to have a good idea of how sensible I > can expect the results to be (in comparison to experimental results). > Could you suggest some recent review papers on applications of this > theory, please? As far as the review papers go I would to thank Mark Thompson and Geoff Hutchison for pointing me to Accurate Prediction of Band Gaps in Neutral Heterocyclic Conjugated Polymers Geoffrey R. Hutchison, Mark A. Ratner and Tobin J. Marks J. Phys. Chem. A (2002) 106(44) p. 10596-10605. the paper compares ZINDO/RPA, HF/RPA and TDDFT/RPA (among other methods) on 60 conjugated organics using AM1 and DFT geometries . Best wishes, Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam$at$dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK mobile: +44-7739-330511 WA4 4AD ======================================================================== From chemistry-request@ccl.net Mon Jun 9 13:35:34 2003 Received: from kff1.uchicago.edu (kff1.uchicago.edu [128.135.160.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59HZYkr001168 for ; Mon, 9 Jun 2003 13:35:34 -0400 Received: from kff1.uchicago.edu (localhost [127.0.0.1]) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.4) with ESMTP id h59HZYfA003482 for ; Mon, 9 Jun 2003 12:35:34 -0500 Received: from localhost (cmtaylor@localhost) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.4) with ESMTP id h59HZWbS003478 for ; Mon, 9 Jun 2003 12:35:34 -0500 Date: Mon, 9 Jun 2003 12:35:32 -0500 (CDT) From: caroline taylor To: CCL list Subject: CCL: ifc -O0 failure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We have run into an anomoly using the ifc compiler with optimization. When builing the code we've been using to benchmark, we've used the various optimization flags, with the following results (numerical result and runtime): -O0: 6.710886E+07 (21.960u 0.020s 0:22.19 99.0%) -O1: 1.718282E+08 (17.560u 0.010s 0:17.76 98.9%) -O2: 1.718282E+08 (17.550u 0.010s 0:17.74 98.9%) -O3: 1.718282E+08 (17.580u 0.000s 0:17.75 99.0%) -O4: 1.718282E+08 (17.570u 0.000s 0:17.75 98.9%) The 0 level optimization is clearly inconsistent, and far larger than round off. This has been checked on multiple machines (all linux). Has anyone run into this before? Is there a known problem with this level, or is something else going on? The very simple code we've used for checking the compiler is below: PROGRAM tyme IMPLICIT NONE REAL :: sum INTEGER :: i INTEGER, PARAMETER :: imax = 100000000 sum = 0.0 DO i = 1, imax sum = sum + DEXP( DBLE(i)/DBLE(imax) ) END DO write(*,*) sum, i END PROGRAM tyme Thanks for your time! Caroline --------------------------------------------- Dr. Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 --------------------------------------------- From chemistry-request@ccl.net Mon Jun 9 14:41:14 2003 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h59IfDkr004755 for ; Mon, 9 Jun 2003 14:41:14 -0400 Received: from alexg (ras4.icp.rssi.ru [194.85.223.84] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Mon, 9 Jun 2003 22:39:44 +0000 Message-ID: <05c301c32eb7$5ae1dbb0$54df55c2@alexg> Reply-To: "Alex. A. Granovsky" From: "Alex. A. Granovsky" To: "CCL_posting" Subject: CCL: PC GAMESS v. 6.3 is available Date: Mon, 9 Jun 2003 22:45:51 +0400 Organization: MSU MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear GAMESS users, the final PC GAMESS version 6.3 is now ready and can be downloaded from the PC GAMESS page at ISU: http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml The PC GAMESS homepage at MSU will be updated accordingly within couple of weeks. Best regards, Alex A. Granovsky, The PC GAMESS project. From chemistry-request@ccl.net Mon Jun 9 14:49:29 2003 Received: from ned.sims.nrc.ca (ned.SIMS.nrc.ca [132.246.109.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59InTkr006111 for ; Mon, 9 Jun 2003 14:49:29 -0400 Received: from ned.sims.nrc.ca (localhost [127.0.0.1]) by ned.sims.nrc.ca (8.12.6/8.12.6/SuSE Linux 0.6) with ESMTP id h59InSbb027709; Mon, 9 Jun 2003 14:49:28 -0400 Received: from localhost (ps@localhost) by ned.sims.nrc.ca (8.12.6/8.12.6/Submit) with ESMTP id h59InSk9027706; Mon, 9 Jun 2003 14:49:28 -0400 Date: Mon, 9 Jun 2003 14:49:28 -0400 (EDT) From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii..at..nrc.ca To: caroline taylor cc: CCL list Subject: Re: CCL:ifc -O0 failure In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS - amavis-milter (http://www.amavis.org/) On Mon, 9 Jun 2003, caroline taylor wrote: > -O0: 6.710886E+07 (21.960u 0.020s 0:22.19 99.0%) > -O1: 1.718282E+08 (17.560u 0.010s 0:17.76 98.9%) > The 0 level optimization is clearly inconsistent, and far larger than > round off. This has been checked on multiple machines (all linux). > > Has anyone run into this before? Is there a known problem with this level, > or is something else going on? Caroline, There is nothing wrong with ifc in this case - your program is badly broken, and should not be relied upon to produce -any- definite answer. You are trying to accumulate numbers, which deviate from one in the 7-th decimal digit. However, you chose to use a type (REAL), which is only accurate to 6-7 decimal digits. Obviously, you should not expect to get any significant digits in the result. With optimizations turned on, ifc carries the accumulation at higher 80-bit precision (which is arguably allowed by the standard), which -accidentally- leads to a result close to the mathematically exact value. If you change your SUM to DOUBLE PRECISION, you will get the answer of 171828183.705001 as an answer for ifc -O0 - which is reasonably close to the formal result of 171828183.705045439197452888531281012... Incidentally, if you try to use this loop for timing purposes, this is not necessarily a good idea - a sufficiently smart compiler could realise that the exact result is given by: (E - 1) E**(1/100000000) ------------------------ E**(1/100000000) - 1 and completely eliminate the loop. Serguei From chemistry-request@ccl.net Mon Jun 9 14:07:24 2003 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59I7Okr002864 for ; Mon, 9 Jun 2003 14:07:24 -0400 Received: from adenine.cgl.ucsf.edu (localhost [127.0.0.1]) by adenine.cgl.ucsf.edu (8.12.9/8.12.9/GSC1.16) with ESMTP id h59I7NSW833725; Mon, 9 Jun 2003 11:07:23 -0700 (PDT) Received: (from meng@localhost) by adenine.cgl.ucsf.edu (8.12.9/8.12.9/Submit) id h59I7Na5878539; Mon, 9 Jun 2003 11:07:23 -0700 (PDT) Date: Mon, 9 Jun 2003 11:07:23 -0700 (PDT) From: Elaine Meng Message-Id: <200306091807.h59I7Na5878539*at*adenine.cgl.ucsf.edu> To: chemistry*at*ccl.net, meng*at*cgl.ucsf.edu Subject: Chimera molecular modeling system The UCSF Resource for Biocomputing, Visualization, and Informatics is pleased to announce the newest release of UCSF Chimera, an interactive molecular modeling system. It is free to academic and non-profit users and is available for Windows, Linux, Mac OS X, IRIX, and Tru64 Unix. It can be downloaded from http://www.cgl.ucsf.edu/chimera Chimera has the capabilities common to many molecular graphics programs, as well as a number of more unique features, including: - Display of multiple sequence alignments and associated structures, with information flow in both directions - Atom-type identification within arbitrary molecules - Hydrogen-bond identification using crystallographically-derived distance and angle criteria - Display of 3-dimensional data sets as contour surfaces or transparent solids, with interactive threshold adjustment - Playback of molecular dynamics trajectories (AMBER format; others forthcoming) - Interface to facilitate screening of candidate ligands from DOCK, including filtering by number/position of hydrogen bonds - Extensibility as a design principle, allowing users to create custom modules without changing Chimera code Further description of Chimera's features can be found at http://www.cgl.ucsf.edu/chimera ------------- On behalf of the Chimera development team, Elaine Meng meng*at*cgl.ucsf.edu Computer Graphics Laboratory, RBVI University of California, San Francisco From chemistry-request@ccl.net Mon Jun 9 14:54:59 2003 Received: from web21201.mail.yahoo.com (web21201.mail.yahoo.com [216.136.129.59]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h59Iswkr006523 for ; Mon, 9 Jun 2003 14:54:59 -0400 Message-ID: <20030609185458.35322.qmail*at*web21201.mail.yahoo.com> Received: from [129.109.73.75] by web21201.mail.yahoo.com via HTTP; Mon, 09 Jun 2003 11:54:58 PDT Date: Mon, 9 Jun 2003 11:54:58 -0700 (PDT) From: IEJMD Subject: CCL: Electronic Conference of Molecular Design To: chemistry*at*ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Call for papers Internet Electronic Conference of Molecular Design 2003 IECMD 2003, October 26 - November 8 An Electronic conference for presenting and discussing recent developments in Molecular Design will be held during October 26 - November 8 2003, on the World-Wide Web. IECMD 2003 covers all areas of molecular design and uses the Internet for exchanging chemical information. Paper Submission Papers (research notes, full papers or reviews) should be submitted as Word files to biochempress*at*yahoo.com. All papers will be peer reviewed. Accepted papers will be published as PDF files on the IECMD 2003 Web site, http://www.biochempress.com. There will be no registration for visitors of IECMD 2003, and all PDF papers will be free for download. After the Conference, all accepted papers will be published in IEJMD - the Internet Electronic Journal of Molecular Design. Important Dates September 1, 2003 - Titles and authors due October 1, 2003 - Papers due, for peer review October 15, 2003 - Final Papers due October 26, 2003 - Conference begins November 8, 2003 - Conference ends For detailed Instructions for Authors, see http://www.biochempress.com Instruction for authors and a Word template for preparing the paper are available for download. IECMD 2003 will cover all aspects of computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: Computer-aided organic synthesis Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods Definition, calculation and evaluation of novel structural descriptors Chemical database searching, clustering, similarity and diversity measure Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) Quantitative Structure-Activity Relationships (QSPR) models for biological activity, toxicity, mutagenicity, and carcinogenicity Prediction of chromatographic retention parameters and design of stationary phases for chromatography Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm Design of special materials, catalysts, high energy compounds, polymers, molecular machines __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From chemistry-request@ccl.net Mon Jun 9 09:46:03 2003 Received: from web13407.mail.yahoo.com (web13407.mail.yahoo.com [216.136.175.65]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h59Dk2kr020984 for ; Mon, 9 Jun 2003 09:46:03 -0400 Message-ID: <20030609134602.88974.qmail*at*web13407.mail.yahoo.com> Received: from [129.237.101.10] by web13407.mail.yahoo.com via HTTP; Mon, 09 Jun 2003 06:46:02 PDT Date: Mon, 9 Jun 2003 06:46:02 -0700 (PDT) From: quch quch Subject: Re: CCL:Some questions about CoMFA To: Jinsong Zhao , CCL In-Reply-To: <20030609094805.80066.qmail*at*web15209.mail.bjs.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Best on your description on your data, you should try something different rather than CoMFA. Also one important thing that you need to check is to make sure that all you data are collected in the same experimental condition, at least for the same set. --- Jinsong Zhao wrote: > Dear all, > > I am a newbie to Tripos's Sybyl, thus I have some > questions about CoMFA. Would you like to give me a > hand? Thanks in advance! > > I have more than two hundred compounds that I hope > to > carry out CoMFA in order to establish a QSAR model. > I > am going to divide the large data set to two parts, > one for training, and the other for validation. > > The first question is whether the alignment should > be > done with a whole data set or with two separated > data > sets (i.e. training and validation data set). > > The second question is what are the alignment rules. > > The third question is how to improve the Q2 or r2. > Because the data set includes compounds with a > diversity of structure, I hope to find a way to > distinguish which are the outliers. > > Thank you very much for your consideration on this > matter! > > Best regards, > > Jinsong > > _________________________________________________________ > Do You Yahoo!? > AwA,MxBgJ@=g5D!0Dc!1JGK-#? > http://cn.rd.yahoo.com/mail_cn/tag/?http://cn.surveys.yahoo.com/cn_user_profile_study_may2003 > > > -= This is automatically added to each message by > 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) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From chemistry-request@ccl.net Mon Jun 9 15:13:06 2003 Received: from kff1.uchicago.edu (kff1.uchicago.edu [128.135.160.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59JD6kr007408 for ; Mon, 9 Jun 2003 15:13:06 -0400 Received: from kff1.uchicago.edu (localhost [127.0.0.1]) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.4) with ESMTP id h59JD6fA004805 for ; Mon, 9 Jun 2003 14:13:06 -0500 Received: from localhost (cmtaylor@localhost) by kff1.uchicago.edu (8.12.3/8.12.3/Debian-6.4) with ESMTP id h59JD6qq004801 for ; Mon, 9 Jun 2003 14:13:06 -0500 Date: Mon, 9 Jun 2003 14:13:06 -0500 (CDT) From: caroline taylor To: CCL list Subject: CCL: ifc -O0 _not_ broken Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to all of you who spotted the flaw in our benchmark code -- turns out that the compiler is fine, and we missed something obvious. Thank you all for your help! Caroline --------------------------------------------- Dr. Caroline M. Taylor Department of Chemistry University of Chicago, James Franck Institute 5640 S. Ellis Avenue Chicago, Illinois 60637 (773) 702-7223 --------------------------------------------- From chemistry-request@ccl.net Mon Jun 9 16:42:24 2003 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h59KgNkr010999 for ; Mon, 9 Jun 2003 16:42:23 -0400 Received: (from mn1@localhost) by helix.nih.gov (8.11.6p2/8.11.6) id h59KgMf1839218; Mon, 9 Jun 2003 16:42:22 -0400 (EDT) Date: Mon, 9 Jun 2003 16:42:22 -0400 From: "M. Nicklaus" To: Noriaki Ikuta cc: chemistry/at/ccl.net, "M. Nicklaus" Subject: Re: CCL:ic50 values in dtp aids dataset In-Reply-To: <20030529184200.75383.qmail/at/web20511.mail.yahoo.com> Message-ID: References: <20030529184200.75383.qmail/at/web20511.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII "IC50", in *this* context, means indeed "concentration of compound that inhibits the growth of uninfected cells by 50%." It is essentially the toxicity of the compound (for uninfected, i.e. healthy cells). The categorization of anti-HIV activity (CI, CM, CA) is derived from the *combination* of the IC50 and EC50 (cell-protection) curves: Only if the antiviral activity of the compound sets in at a substantially lower concentration than the toxicity can the compound be termed active in the cell-based assay, otherwise you're just killing the cell. That's why, indeed, you cannot categorize the compounds by IC50 alone. A bit more information on this, including some references, can be found at http://dtp.nci.nih.gov/docs/aids/aids_screen.html. Hope this helps, Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1/at/helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ On Thu, 29 May 2003, Noriaki Ikuta wrote: > Paul Hawkins thank you for your respond. > > But it seems to be imposible the categorise the compounds based on the > provided IC50 values. The ranges do significantly overlapp. > > categy mean min max #cmpds (several outliers are left out) > CA -4.5 -7.0 -2.5 705 > CM -4.0 -7.4 -2.7 1360 > CI -4.0 -10.0 -1.9 36289 > NA -4.4 -7.3 -3.0 294 > > Note on reliability: > The expression "Log10HiConc - Log10IC50 > 1.0" is only met in roughly 18% > of the cases. How useful are those IC50 values at all? > > Noriaki > > > --- Paul Hawkins wrote: > > Noriaki, > > > > I suspect the statement > > > > "concentration of compound that inhibits the growth of uninfecte > > cells by 50%" > > > > is a typo. IC50 is the concentration of a compound required to reduce > > the > > readout of the assay by 50%, whether you are measuring enzyme activity, > > receptor activation or cell growth/division. > > The classification into the different activity classes is somewhat > > arbitrary. Generally speaking a compound having an IC50 greater than > > 10^-5 > > is not considered active as the doses required to achieve those > > concentrations in an animal (let alone a human) would be huge. For > > comparison most anti-HIV drugs on the market now have IC50's in this > > sort of > > assay around 10^-6 and have IC50's against their target receptor (the > > protease or reverse transcriptase mostly) in the 10^-9 range. > > There may also be a known correlation between IC50's in this assay and > > doses > > required to cause remission of infection in an animal model of HIV in > > humans > > and again the maximum acceptable dose may translate to an IC50 in this > > assay > > of 10^-5. > > I am unaware of any papers on this dataset in particular though a good > > many > > studies have used this dataset for various purposes. > > > > One word of warning Log10HiConc should always be around 10x greater than > > the > > IC50 so as the Log10HiConc approaches the reported IC50 the IC50 result > > becomes less and less reliable. > > > > Paul Hawkins > > Applications Scientist > > Tripos Inc > > 1699 South Hanley Road > > St. Louis MO 63144 > > > > Ph: 617-899-4151 > > E-mail: phawkins/at/tripos.com > > > > www.tripos.com > > > > > __________________________________ > Do you Yahoo!? > Yahoo! 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