From chemistry-request@server.ccl.net Thu Feb 14 22:51:05 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1F3p5Z30869 for ; Thu, 14 Feb 2002 22:51:05 -0500 Received: from eden.rutgers.edu (narnia2.rutgers.edu [165.230.180.158]) by goshen.rutgers.edu (Postfix) with ESMTP id 892351FC56 for ; Thu, 14 Feb 2002 22:50:48 -0500 (EST) Received: from azrael1.rutgers.edu (azrael1.rutgers.edu [165.230.4.120]) by eden.rutgers.edu (Postfix) with SMTP id A56F0A29B3 for ; Thu, 14 Feb 2002 22:50:46 -0500 (EST) From: To: chemistry@ccl.net Subject: The perspective of molecular docking:A killer application to drug design is emerging Date: Thu, 14 Feb 2002 22:50:00 -0500 (EST) X-Real-Sender: jianquan@eden.rutgers.edu X-Mailer: Postman 1.10 Message-ID: <5351791216jianquan@eden.rutgers.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1F3p5Z30870 The perspective of molecular docking: A killer application to drug design is emerging by Jianquan Chen Email: chen_jianquan@yahoo.com As structural genomics initiative begins to bring more and more 3D macromolecular structures, the work involved to validate all these potential targets, to demonstrate their therapeutic relevance, and to find leads will become heavily dependent on the high-throughput screening technologies such as automated molecular docking. Now it makes more and more chemical compounds screened because a new drug has to meet more and stricter requirements. Thus high-throughput screening (HTS) technology has played an increasingly important role in new drug development. And for many pharmaceutical companies, HTS is now an essential component to identify leads. Molecular docking over a large scale virtual compound database is a kind of virtual HTS technology. Molecular docking is used to predict the bound conformation of the ligand to the receptor. It connects the structural bioinformatics and drug design. Straightforwardly speaking, it is a tool to mine gold from the structural bioinformatics data. It can be divided into 3 classes, rigid ligand/rigid receptor, flexible ligand/rigid receptor, flexible ligand/(partially) flexible receptor docking. Rigid ligand/rigid receptor docking is very fast but not detailed. flexible ligand/ (partially) flexible receptor docking is too complicated to be used to screen a large scale database. So we only discuss flexible ligand/rigid receptor docking. A docking problem can be divided into search algorithm and scoring function. search algorithm should be efficient enough to find the lowest energy configuration or conformation. The scoring function should be able to distinguish a correct binding mode from other putative modes. I only discuss search algorithm here because the progress on the search algorithm and the computer will remove the hardware obstacle for the flexible ligand/ rigid receptor docking to enter the medicinal chemistry lab soon. AEDock1.1, a new release of AEDock, where a new technology is introduced, can dock XK263, a bulky ligand with 10 rotatable bonds, into HIV-1 protease in 23.4 seconds using a tolerance of 0.01nm rmsd with a success rate of 92% on a PC with an AMD 750M CPU+256M SDRAM. Please read the results of AEDock1.1 at http://www20.brinkster.com/jianquan/aedock11/default.asp .It is a WHOLE MOLECULE-BASED docking program and so avoids the disadvantages of the fragment-based docking approaches. Based on the rotatable bond distribution table from Bohdan W., it is estimated that 2 PC with 2.2GHz Intel CPU can screen 1M drug-like compounds with 0-10 rotatable bonds in 1 week. Please follow the above link to see how it is estimated. Comparison of molecular docking and real HTS 1.Molecular docking over a compound database is more productive and cost-efficient than a real HTS. I list the disadvantages of real HTS here: 1. HTS is no guarantee of success. 2. Establishing a robust assay for a new target takes time and money. Hit rates against some receptors are reported to be very low, necessitating screening of very large numbers of com-pounds (tens to hundreds of thousands). Collections of synthesized compounds or natural products often contain far less chemical diversity than is desired, are not bottomless resources, and are very time-consuming to replenish. 3. Techniques such as combinatorial chemistry offer the potential for synthesizing very large libraries of compounds, but in practice this approach is time-consuming for drug-like com-pounds and may still produce libraries of relatively restricted diversity. 4. What is the most important is that a real HTS system and a real compound database are so expensive that only companies can afford them. A normal medicinal chemistry lab can't afford it. Bohdan W. etc. used a 64-processor SGI Origin2000 to dock a 1.1 million drug-like compounds and it took the workstation 6 days to finish the job. These compounds were docked into human alpha-estrogen receptor. after being docked and filtered by some supplementary descriptors, a set comprising 37 commercially available compounds were chosen to be assayed in a standard competitive radio-ligand binding assay. 21 exhibited an inhibition constant ( Ki ) of 300 nM (nanomolar) or less, with the best compounds at 8 nM. Given the structural novelty of the hits (compounds known to possess estrogenic activity or to be structurally similar to known ligands were excluded > from assay), this represents a very positive result, demonstrating that virtual screening can readily identify potent ligands from a variety of structural classes. Maybe you will say:"a 64-processor SGI Origin2000 is very expensive." But if AEDock1.1 is used, then we only need to buy 2 PC 2.2GHz Intel CPU. A Dell Dimension 8200 PC with 2.2G Pentium 4 CPU and 256MB PC800 RDRAM (Rambus dynamic RAM) only costs you $1,689 in Feb 13,2002. The total is about $3,300. Several months later they can be bought at a cheaper price. I predict in the end of 2002 a PC with one single CPU can screen 1M drug-like compounds with 0-10 rotatable bonds using whole molecule- based flexible ligand/rigid receptor docking approach in 1 week because performances of CPU and search algorithm are keeping increasing. It means that the hardware obstacle for the flexible docking/rigid receptor docking to enter normal medicinal chemistry lab will disappear soon. Comparison of molecular docking and pharmacophore queries or focused 2- D property the flexible ligand/rigid docking is more detailed and more objective than pharmacophore queries or focused 2-D property. Application of pharmacophore queries or focused 2-D property profiles may significantly inhibit the diversity of the compound subset because they are biased by the properties of known ligands. In contrast, the molecular docking program can process an entire chemical database with minimal pre-filtering (e.g., to eliminate unstable or toxic moieties) so that the final selection is based on the quality of the docked models rather than a subjective opinion of what properties are expected in a ligand. This route is a very promising one to find structurally novel ligands, which may make receptor interactions similar to known ligands. The roles molecular docking plays in the drug design 1. find leads. 2. provide groups for chemists to modify the leads. When compounds are docked into the receptor, the groups interacting with the subsites of the receptor should be ranked. Maybe the groups with good ranking plus leading compounds will lead to final products. (up to now I didn't find any paper on this role of the molecular docking, please tell me if you find any paper on this. ) So molecular docking provides not only leading compounds, but also suggest you how to modify the leads. Oops, molecular docking provides a whole solution for drug discovery. It sounds molecular docking very promising and will be popular soon. Then why not to invest your money or energy in it? Please contact me if you are interested. Email:chen_jianquan@yahoo.com, Phone:(USA)732- 207-8147 In a word, the molecular docking will become a killer application to drug design. It will enter the normal medicinal chemistry labs, not only the big pharmaceutical companies. The obstacles for the molecular docking to enter the medicinal chemistry lab 1. The virtual compound database. Now most of the scientist uses ACD-3D or ACD-SC from MDL as the compound database for screening. It will cost you about $15,000 to get a license of ACD-3D and ACD-SC on a single "Datastation" per year. But MDL allows you to share the ISIS databases with other scientists and so it will lower your cost. In addition you need a license of Enterprise Oracle database. It seems the database costs you lots of money. There is an alternative solution. A free NCI 3D compound database can be stored in free database such as Mysql. After being screened the final set of compound can be submitted to www.chemexper.com to know if the compound is commercially available. In addition Oracle database is too difficult for a chemist or molecular modeler to maintain. 2. The available 3D macromolecular structures. Most of the 3D structures of macromolecules are not available. Fortunately, ?structural genomics initiative begins to bring more and more 3D macromolecular structures and maybe computational protein folding will bring some reliable structures. 3. The scoring functions and the accuracy of the 3D macromolecular structures. Not all crystallographic structures can be reproduced because the scoring function can't distinguish a correct binding mode from other putative modes for some cases or some crystallographic structures are not accurate enough. Please tell me that if you any paper on test a scoring functions using hundreds of PDB entries. Please sent comments to chen_jianquan@yahoo.com or visit http://www20.brinkster.com/jianquan/aedock11/default.asp or my homepage (http://www-ec.njit.edu/~jc26/). Note:(1) some contents are extracted from "Large-scale virtual screening for discovering leads in the postgenomic era", Waszkowycz, B.; Perkins, T. D. J.; Sykes, R. A.; Li, J. . IBM SYSTEMS J., 2001, 40, 360-376. (2) please include the web address of this paper (http://www20.brinkster.com/jianquan/aedock11/perspective.asp) and my name if you want to cite the opinions in this paper. From chemistry-request@server.ccl.net Fri Feb 15 02:41:17 2002 Received: from mail.univ-reims.fr ([193.50.208.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1F7fHZ01940 for ; Fri, 15 Feb 2002 02:41:17 -0500 Received: from [194.199.64.95] (i95.univ-reims.fr [194.199.64.95]) by mail.univ-reims.fr (8.11.2/8.11.1) with ESMTP id g1F7Q7i04031 for ; Fri, 15 Feb 2002 08:26:07 +0100 (MET) User-Agent: Microsoft-Entourage/10.0.0.1309 Date: Fri, 15 Feb 2002 08:26:50 +0100 Subject: G98 and SGE From: Etienne Derat To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1F7fHZ01941 Dear CCLers Is there someone who uses Gaussian98 with the batch system from SUN i.e. Sun Grid Engine? When we launch G98 jobs who request more than one processor with SGE, they all fail. In interactif mode (without SGE) there is no problem. For information, the computer is SMP. Thanks for all, Etienne -- Etienne Derat Doctorant Groupe Modélisation et Réactivité Chimique UMR 6519 "Réactions sélectives et Applications" Université de Reims Champagne-Ardenne France Tél : +33 3 26 91 32 45 Fax : +33 3 26 91 31 66 From chemistry-request@server.ccl.net Fri Feb 15 10:38:40 2002 Received: from mail-01.med.umich.edu ([141.214.93.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FFceZ14424 for ; Fri, 15 Feb 2002 10:38:40 -0500 Received: from gwia-01-MTA by mail-01.med.umich.edu with Novell_GroupWise; Fri, 15 Feb 2002 10:38:17 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.1 Date: Fri, 15 Feb 2002 10:38:05 -0500 From: "Renxiao Wang" To: Subject: =?Windows-874?Q?MDL#=20=97>=20CAS#=20=3F=3F=3F?= Mime-Version: 1.0 Content-Type: text/plain; charset=Windows-874 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g1FFceZ14425 Hi, CCLers! There are a number of compounds that we would like to obtain and test in our bioassays. But for some reasons we only know the MDL catalog numbers of these compounds. We are wondering if there is any website which can perform a convenient MDL# —> CAS# conversion? Please note that we are looking for something other than the MDL/ISIS system. Any clue will be highly appreciated! We will put back the summary if the answers are informative. Best regards, Renxiao Wang, Ph.D. University of Michigan Medical School From chemistry-request@server.ccl.net Fri Feb 15 08:26:17 2002 Received: from gate.boehringer-ingelheim.de ([148.188.1.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g1FDQHZ10710 for ; Fri, 15 Feb 2002 08:26:17 -0500 Received: from bibex01.bc.de.bic by gate.boehringer-ingelheim.de via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 15 Feb 2002 13:24:04 UT Received: by bibex01.eu.boehringer.com with Internet Mail Service (5.5.2653.19) id <1NL316ZY>; Fri, 15 Feb 2002 14:25:58 +0100 Message-ID: From: Christian.Pilger@bc.boehringer-ingelheim.com To: chemistry@ccl.net Subject: aqueous solubilities of organic compounds Date: Fri, 15 Feb 2002 14:25:58 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear CClers, currently I'm looking for methods and datasets for the prediction of aqueous solubilities of organic (preferrably drug like) compounds. Though I gained an overview about the literature published in this field and commercial solutions offered to solve this problem, I doubt that this overview is complete yet. Thus I would like to ask for your advice: are you aware of methods to predict solubility ? Are you interested in an exchange of experience dealing with different methods ? Did you ever come across databases with experimentally determined solubilities, which might be accessible ? Do you have own datasets, which you are willing to share ? Looking forward to hearing from you - all comments are appreciated. I will provide a summary to the list. Sorry, if you received multiple copies of the mail. Cheers, Christian ________________________________________________________________ Dr. Christian Pilger Dept. Chemical Research / Structural Research J51-00-01 Boehringer Ingelheim Pharma KG D-88397 Biberach/Germany Phone: 07351-545749 Fax: 07351-5497924 mailto: christian.pilger@bc.boehringer-ingelheim.com From chemistry-request@server.ccl.net Fri Feb 15 05:59:17 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FAxGZ07414 for ; Fri, 15 Feb 2002 05:59:16 -0500 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP; Fri, 15 Feb 2002 11:58:46 +0100 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id LAA05153; Fri, 15 Feb 2002 11:58:45 +0100 (MET) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Fri, 15 Feb 2002 11:58:44 +0100 (MET) From: Eugene Leitl X-X-Sender: ui22204@sun4.lrz-muenchen.de To: CHEMICAL INFORMATION SOURCES DISCUSSION LIST cc: chemistry@ccl.net Subject: boost for research paper access Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII http://news.bbc.co.uk/hi/english/sci/tech/newsid_1818000/1818652.stm By BBC News Online's Ivan Noble Plans to extend free access to scientific and academic research papers have received a boost with the announcement of a $3m grant from financier and philanthropist George Soros' Open Society Institute. The literature that should be freely accessible online is that which scholars give to the world without expectation of payment Budapest Open Access Initiative Open access advocate Professor Stevan Harnad of the University of Southampton, UK, says the money could make it easier for academics wanting to set up their own alternatives to commercially run journals. "The vast potential benefits of open access to research and researchers are already there... but the subsidy lowers the entry barriers for would-be open-access initiatives," he said. Critics of commercial journals say their subscription charges hamper research at institutes and in countries where research budgets are tight. They say that researchers write and review papers for free, so the journals should not charge to read them. "They don't want to get paid, what they want is that other researchers should read and use their work," Professor Harnad told BBC News Online. "The fact that their literature is treated for trade is anathema," he said. Budapest declaration Some commercial journals have extended the amount of literature they make available for free in response to a boycott campaign by scientists calling themselves the Public Library of Science. But journal publishers defend their charges as necessary to finance their operations. The new money for open alternatives comes as part of a new declaration called the Budapest Open Access Initiative, signed by dozens of institutions and hundreds of researchers. They say they are not opposed to commercial journals, but want to see an alternative system of free access journals and self- archiving set up in parallel. "The literature that should be freely accessible online is that which scholars give to the world without expectation of payment," reads the declaration. It calls for "free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose". Seed money Professor Harnad's colleagues Chris Gutteridge and Rob Tansley developed a piece of software called Eprints, which, they hope, makes the process of publishing easier and therefore cheaper. He says the Soros money could be used to "seed" schemes where academics will pay a small fee to have their papers reviewed but users will pay nothing to read them. "To start up and fill an institutional Eprint Archive costs less than $10,000; to start up and fill an alternative journal costs less than $50,000; so $3m can do a lot of good in three years," he says. More important though than the money, he adds, is for there to be a critical mass of research available from free archives online. "It's a question of when the dominos start falling," he said. From chemistry-request@server.ccl.net Fri Feb 15 11:28:05 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FGS5Z16004 for ; Fri, 15 Feb 2002 11:28:05 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id LAA28073; Fri, 15 Feb 2002 11:27:43 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3C6D2D97.6BC72D4B@cornell.edu> Date: Fri, 15 Feb 2002 10:47:36 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CHARMm help needed again Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all A colleague of mine has a slight problem that I have been brought in to help with and I am stumped. Apparently, there was a subroutine developed in CHARMm called SBOUND which is supposed to allow the user to specify the use of a spherical, cubic, or plane potential. Well, we have learned (we think) that SBOUND contains an "undefined" variable called IBOUND, which is what allows the choice of spherical (IBOUND=1), cubic (IBOUND=2) or planar (IBOUND=3) potentials. Thus, since IBOUND is not defined anywhere in the program (at least as far as SBOUND is concerned; there is an IBOUND used in an unrelated subroutine as an array) we cannot use "SBOUND", so we have to input the potential in another way. The question I have is this. We have a "file" that defines a spherical potential. Does anyone out there know how we can generate a file having a planar potential, or does someone have a palnar potential file in the "correct" format that we could use? I would think that since there are many users of CHARMm out there that someone has encountered this problem before so that we don't have to reinvent the wheel. (BTW, I have seen Brooks' and Karplus's paper in J. Chem. Phys, vol. 79, pp 6312 - 6325.) Thanks in advance, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri Feb 15 12:06:16 2002 Received: from adenine.cgl.ucsf.edu ([128.218.27.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FH6GZ16834 for ; Fri, 15 Feb 2002 12:06:16 -0500 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by adenine.cgl.ucsf.edu (8.12.2/8.12.2/GSC1.13) with ESMTP id g1FH5wl7598577; Fri, 15 Feb 2002 09:05:58 -0800 (PST) Message-Id: <200202151705.g1FH5wl7598577@adenine.cgl.ucsf.edu> To: Eugene Leitl cc: CHEMICAL INFORMATION SOURCES DISCUSSION LIST , chemistry@ccl.net Subject: Re: CCL:boost for research paper access In-Reply-To: Your message of "Fri, 15 Feb 2002 11:58:44 +0100." Date: Fri, 15 Feb 2002 09:05:58 -0800 From: "David Konerding, Ph.D." Eugene Leitl writes: > >"The literature that should be freely accessible online is that which >scholars give to the world without expectation of payment," reads the >declaration. That's known as altruism. I don't know any scientists who publish anything without some expectation of payment- in the form of credit, attention, or money. > >It calls for "free availability on the public internet, permitting any >users to read, download, copy, distribute, print, search, or link to the >full texts of these articles, crawl them for indexing, pass them as data >to software, or use them for any other lawful purpose". As much as this sounds like a good idea, making journal articles freely available on the internet has a lot of hidden costs. Providing the web server hardware, internet connectivity, and maintaining the site are only the first costs that come to mind. Making sure the articles aren't written by cranks who can produce semi-scientific sounding text that means absolutely nothing has a cost- you have to hire somebody who's an expert in that area. George Soros has a lot of money- probably enough to float a project like this for many years- but I don't really expect the service to be "free" nor do I expect these free online journals to ever achieve the prominence (IE influenceable readership) that some print journals have. From chemistry-request@server.ccl.net Fri Feb 15 12:31:03 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FHV2Z17418 for ; Fri, 15 Feb 2002 12:31:02 -0500 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP; Fri, 15 Feb 2002 18:30:42 +0100 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id SAA06413; Fri, 15 Feb 2002 18:30:41 +0100 (MET) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Fri, 15 Feb 2002 18:30:40 +0100 (MET) From: Eugene Leitl X-X-Sender: ui22204@sun4.lrz-muenchen.de To: "David Konerding, Ph.D." cc: Eugene Leitl , CHEMICAL INFORMATION SOURCES DISCUSSION LIST , Subject: Re: CCL:boost for research paper access In-Reply-To: <200202151705.g1FH5wl7598577@adenine.cgl.ucsf.edu> Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 15 Feb 2002, David Konerding, Ph.D. wrote: > That's known as altruism. I don't know any scientists who publish > anything without some expectation of payment- in the form of credit, > attention, or money. Do I publish or act as a reviewer in Nature or JACS for the financial gain? Hardly. Credit/attention is reputation, and is orthogonal to the medium being commercial. It's just commercial journals were there first, and have accrued reputation themselves. It can be argued that e.g. http://xxx.lanl.gov has by now attracted sufficient amount of reputation that authors can begin accruing reputation based on a (preferably, digitally signed) published paper trail. The reason this has not happened yet is that the users are conservative or simply unaware of the possibilities. Clearly, established journals also have an interest in locking their user base, e.g. by not accepting papers already published in an electronic preprint archive. Writing papers takes effort, so a user would tend to submit good papers to a high-impact journal for the sake of securing her grants. > As much as this sounds like a good idea, making journal articles freely > available on the internet has a lot of hidden costs. Providing the web > server hardware, internet connectivity, and maintaining the site are First two items can be had for about $10/month on the free market right now. The incremental costs are negligable in the current academic and industrial IT infrastructure. The costs to you are zero if you're using an existing service such as xxx.lanl.gov > only the first costs that come to mind. Making sure the articles aren't Site administration is negligable, if papers are submitted via a simple interface by the authors themselves (or their grad students), and published semiautomatically. http://lanl.arxiv.org/help/submit > written by cranks who can produce semi-scientific sounding text that > means absolutely nothing has a cost- you have to hire somebody who's an > expert in that area. xxx.lanl.gov is not a refereed site. It is of course possible to transparently add such a layer to an existing publishing service, which may or may not be commercial. Collaborative consensus filtering should be sufficient to remove the bulk of cranks and kooks by an enduser-driven process. > George Soros has a lot of money- probably enough to float a project like > this for many years- but I don't really expect the service to be "free" > nor do I expect these free online journals to ever achieve the > prominence (IE influenceable readership) that some print journals have. I think chemists are just more conservative that the average xxx.lanl.gov user. From chemistry-request@server.ccl.net Fri Feb 15 15:16:53 2002 Received: from red.CACheSoftware.com (IDENT:root@[12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1FKGrZ21387 for ; Fri, 15 Feb 2002 15:16:53 -0500 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g1FKF7d06754; Fri, 15 Feb 2002 12:15:07 -0800 Message-Id: <5.1.0.14.0.20020215120213.02a7aaf0@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 15 Feb 2002 12:19:33 -0800 To: Christian.Pilger@bc.boehringer-ingelheim.com From: David Gallagher Subject: Re: CCL:aqueous solubilities of organic compounds Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Christian, There is a zipped file which includes a water solubility QSPR along with the calibration set of 156 environmentally significant organic molecules and water solubility data available at: http://www.cachesoftware.com/downloads/LogW.zip The QSPR uses descriptors calculated by MOPAC-COSMO. The r^2 correlation is 0.95. It is located on: http://www.cachesoftware.com/cache/applications.shtml If you do not already have the CAChe software to open the files, you can download a free evaluation copy from the same site. David Gallagher, Fujitsu At 02:25 PM 2/15/2002 +0100, Christian.Pilger@bc.boehringer-ingelheim.com wrote: >Dear CClers, > > currently I'm looking for methods and datasets for the prediction of >aqueous solubilities of organic (preferrably drug like) compounds. Though I >gained an overview about the literature published in this field and >commercial solutions offered to solve this problem, I doubt that this >overview is complete yet. Thus I would like to ask for your advice: are you >aware of methods to predict solubility ? Are you interested in an exchange >of experience dealing with different methods ? Did you ever come across >databases with experimentally determined solubilities, which might be >accessible ? Do you have own datasets, which you are willing to share ? > >Looking forward to hearing from you - all comments are appreciated. I will >provide a summary to the list. Sorry, if you received multiple copies of the >mail. > >Cheers, > >Christian >________________________________________________________________ > > Dr. Christian Pilger > > Dept. Chemical Research / Structural Research > J51-00-01 > Boehringer Ingelheim Pharma KG > D-88397 Biberach/Germany > Phone: 07351-545749 > Fax: 07351-5497924 > mailto: christian.pilger@bc.boehringer-ingelheim.com > From chemistry-request@server.ccl.net Fri Feb 15 23:59:39 2002 Received: from nanolc.jst.go.jp ([202.241.21.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g1G4xcZ31390 for ; Fri, 15 Feb 2002 23:59:39 -0500 Received: (from yoneya@localhost) by nanolc.jst.go.jp (8.11.6/3.7W) id g1G4xJk29453; Sat, 16 Feb 2002 13:59:19 +0900 (JST) Date: Sat, 16 Feb 2002 13:59:19 +0900 (JST) Message-Id: <200202160459.g1G4xJk29453@nanolc.jst.go.jp> To: chemistry@ccl.net Cc: yoneya@nanolc.jst.go.jp Subject: 2-D XRD pattern software From: yoneya@nanolc.jst.go.jp X-Mailer: mnews [version 1.22PL4] 2000-05/28(Sun) Dear CCL peoples: Does anybody knows freewares to calculate 2-D X-ray diffraction patterns from atomic coordinates/trajectory generated by MD simulations. Thank you for advance. Makoto Yoneya (Dr.) yoneya@nanolc.jst.go.jp Yokoyama Nano-structured Liquid Crystal Project Tskukuba JAPAN