Subject: What is a random pharmacophor model ? From: Jan Torleif Pedersen Reply-To: jatp$at$lundbeck.com To: chemistry$at$ccl.net Message-Id: <1081975673.1690.35.camel@automatic> Greetings CCL'ers. A question from the philisophical department ! Is anyone aware of what constitutes a 'random' pharmacophore model? That is - what happens if you try to generate pharmacophore models from 200 or some other small number of small molecules selected from a large diverse screening library (ACD,MDDR ..) by random, and you repeat this procedure a large number of times? This ofcourse has to be done with some sort of automatic pharmacophore generation tool - there are a number of those out there. The deeper meaning behind this question is ofcourse to try and understand if one can objectively evaluate the significance of a given pharmacophore model. Many Regards -- Jan Dr. Jan T. Pedersen Section Head, Bioinformatics H. Lundbeck A/S Ottiliavej 9 2500 Valby Denmark phone: 36 43 28 87 email: jatp$at$lundbeck.com From chemistry-request@ccl.net Fri Apr 23 05:12:02 2004 Received: from sigfrido.unito.it (sigfrido.unito.it [130.192.119.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3NABxKC010537 for ; Fri, 23 Apr 2004 05:12:00 -0500 Received: (from root@localhost) by sigfrido.unito.it (8.12.antani) id i3NAD3OQ026338 for chemistry!at!ccl.net; Fri, 23 Apr 2004 12:13:03 +0200 Received: from unito.it (chpc28.ch.unito.it [130.192.118.37])by sigfrido.unito.it (8.12.antani) with ESMTP id i3NAD2Bk026286for ; Fri, 23 Apr 2004 12:13:02 +0200 Message-ID: <4088EBF5.2D74585F!at!unito.it> Date: Fri, 23 Apr 2004 12:12:05 +0200 From: MSSC Organization: Dip. Chimica IFM X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry!at!ccl.net Subject: Local correlation methods: From molecules to crystals Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-scanner: scanned by Inflex 1.0.12.7 X-Spam-Status: No, hits=0.0 required=7.5 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 Local correlation methods: From molecules to crystals LCC2004 September 9-11, 2004 - Torino, Italy http://www.theochem.unito.it/lcc2004 II CIRCULAR Scope of the LCC2004 Workshop Local Correlation techniques permit the accurate and efficient evaluation of post-HF correlation corrections in large molecules. Their adaptation for the solution of the same problem in non-conducting periodic systems is straightforward in principle but technically demanding. Implementation of local-MP2 the simplest form of post-HF ab initio scheme, in connection with the CRYSTAL program (CRYSCOR project) is currently at an advanced stage, as the result of the collaboration between the Theoretical Chemistry Group of the Torino University and scientists from different Institutions (M. Sch|tz, C. Zicovich). The workshop is aimed to analyze the situation in this area of research, to discuss computational strategies, to suggest new developments, to propose applications and to promote new collaborations. It will comprise a number of invited contributions (see below), panel discussions open to all participants, and a poster session. Scientific Committee: Cesare Pisani * Martin Sch|tz Roberto Dovesi * Vic R. Saunders (*) Directors Speakers (in alphabetical order) (*) Provisional titles of presentations Uwe Birkenheuer, Max Planck Institut, Dresden (Germany) Cluster Embedding for Correlation Calculations: Method and Applications Stefano Evangelisti, University of Toulouse (France) Multi-Reference calculations with localized orbitals Robert Evarestov, University of St. Petersburg (Russia) Symmetry of Wannier Functions Peter Fulde, Max Planck Institut, Dresden (Germany) Energy bands based on local correlation methods. Peter Knowles, University of Birmingham (UK) Fred Manby, University of Bristol (UK) Cesare Pisani, Silvia Casassa, Gabriella Capecchi, Roberto Dovesi, University of Torino (Italy) The CRYSCOR project: status and prospects Peter Pulay, University of Arkansas (USA) Toward full-accuracy local correlation methods Vic R. Saunders, University of Torino (Italy) and CCLRC, Daresbury (UK) The use of Pair Natural Orbitals in MP and CC Andreas Savin, University of Paris VI (France) On the adiabatic connection: a link between CI and DFT Martin Sch|tz, University of Stuttgart (Germany) Hermann Stoll, University of Stuttgart (Germany) Many-body expansions in terms of localized orbital groups. Claudio Zicovich-Wilson, University of Morelos (Mexico) (*) All speakers have confirmed their participation. Contact Information and application form: http://www.theochem.unito.it/lcc2004 E-mail: mssc!at!unito.it Telephone: +39 011 670 7562(4) Fax: +39 011 670 7855 Postal address: Workshop04 - Dipartimento di Chimica IFM Via Giuria 5 - I 10125 Torino Italy _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex From chemistry-request@ccl.net Fri Apr 23 02:16:34 2004 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i3N7GWKC003519 for ; Fri, 23 Apr 2004 02:16:33 -0500 Received: from ac12.sci.kun.nl [131.174.179.19] (helo=ac12.sci.kun.nl) by wn1.sci.kun.nl (8.12.10/3.67) with ESMTP id i3N7HREo001312; Fri, 23 Apr 2004 09:17:27 +0200 (MEST) From: "E.L. Willighagen" Reply-To: egonw=at=sci.kun.nl To: Glenn Butterfoss , Subject: Re: CCL:open-pharma? Date: Fri, 23 Apr 2004 09:17:18 +0200 User-Agent: KMail/1.5.4 References: <309710306fc3.306fc3309710=at=med.unc.edu> In-Reply-To: <309710306fc3.306fc3309710=at=med.unc.edu> MIME-Version: 1.0 Content-Type: Text/Plain; charset="iso-8859-1" Content-Description: clearsigned data Content-Disposition: inline Message-Id: <200404230917.26616.egonw=at=sci.kun.nl> X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i3N7GYKC003523 -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 22 April 2004 23:06, Glenn Butterfoss wrote: > The growth of the open-source model of software development has > been (to me) quite astonishing. Recently, it seems the open source > model has evolved to live in new habitats, such as the efforts of > groklaw.net to evaluate intellectual property claims in the Linux > software and wikipedia.com as a general human knowledge base. I am > wondering if (any) CCLers' would consider the idea of open-source > pharmaceutical development , for the computer-based identification of > lead compounds, to be appropriate and/or feasible with current > technology. Drugdesign.org has been mentioned on CCL, but this is more > of a listing of available software ... I have in mind community based > project integrating software development, database construction and > error checking, target identification and therapeutic refinement. This > would, in a sense, be meta -open-source software development ...an > effort to optimize both the programs themselves, methods for using and > combining them, and organization of results. (As far as I know, this has > yet to be tried.) Almost true :) A week ago a QSAR project started which is going provide a general tool to make QSAR/QSPR (etc) models, from setting up a database to validation and application of those models for virtual screening. It is not as broad as the project you propose, but at least a subset of it. This specific project is hosted at http://qsar.sourceforge.net and plans are currently discussed on the email list. The website is being populated next week with ideas discussed on the mailing list. An important feature of this project is that main achievements will be the definition of interfaces (how programs can be accessed) so that any common tool can be integrated into the GUI, and standards for exchanging data between programs. Note that the GUI will be written in Java, so that it will run on all/most platforms. If interested, please join the mailing list. yours sincerely, Egon Willighagen - -- egonw=at=sci.kun.nl PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAiMMFd9R8I9Yza6YRAjdAAKCo8p+pR4OPszt9bR0dd/nRQOy2VwCeIcJO sQjMOSJsdsVCP+C1Lzat4vk= =7ys4 -----END PGP SIGNATURE-----