From owner-chemistry@ccl.net Mon Sep 29 06:36:01 2008 From: "Rene Thomsen rt-$-molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2008 v3.0.0 Message-Id: <-37816-080929063150-23010-uxeua0kMYjpkk31niygfAQ(-)server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 29 Sep 2008 06:31:46 -0400 Sent to CCL by: "Rene Thomsen" [rt- -molegro.com] Aarhus, Denmark, September 29th, 2008 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for predicting protein-ligand interactions available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 3.0: * Displaced Water Model for more accurate modeling of water-mediated ligand interactions: when docking with explicit water molecules, individual water molecules can be displaced by ligands. * Molecular Descriptors: MVD is now able to calculate various molecular descriptors including our own topological CFDM (Chemical Feature Distance Matrix) descriptors. * New protein preparation wizard: it is now easier to validate a target receptor and to inspect and change protonation states. The new preparation dialog also makes it possible to repair, mutate, and minimize sidechains. * The Data Analyzer in MVD has been updated with a Similarity Browser dialog that makes it easy to rank/screen compounds based on similarity to one or more reference ligands. * Minor user interface updates and bug fixes (see Release Notes for details). To download a trial version, please visit our company website at: http://www.molegro.com. For more information contact: Rene Thomsen, CEO Molegro C. F. Moellers Alle, Bldg. 1110 DK-8000 Aarhus Denmark E-mail: rt[]molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon Sep 29 08:58:01 2008 From: "rkolakow##rci.rutgers.edu" To: CCL Subject: CCL:G: Optimization Question/ Hessian Matrix Message-Id: <-37817-080929080644-25467-pT6mV+gSJBoRYgYIYPaYxA^^server.ccl.net> X-Original-From: rkolakow(a)rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 29 Sep 2008 07:32:56 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: rkolakow{=}rci.rutgers.edu Good Morning CCLers, I have been working on a difficult to understand optimization problem. That is, for the life of me I can not rationalize why the molecule's substituents are optimizing in one direction over another. What I would like to do is view the Hessian Matrix and the force constants to observe the atoms interactions during each step of the optimization. Does anyone know how to deconvolute the Hessian Matrix from a .chk G03 file? Thanks, Robert Kolakowski The Department of Chemistry Rutgers, New Brunwick NJ From owner-chemistry@ccl.net Mon Sep 29 10:17:01 2008 From: "Oellien, F (Frank) frank.oellien(a)sp.intervet.com" To: CCL Subject: CCL: 4. German Conference on Chemoinformatics - Call for Registration Message-Id: <-37818-080929100507-27773-1bWQpb8zKvQ2ihZTvsy3JQ]~[server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 29 Sep 2008 15:25:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien(0)sp.intervet.com] CALL FOR REGISTRATION 4th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 9 - 11 November 2008 Dear Colleagues, The CIC division of the German Chemical Society announces the 4. German = Conference on Chemoinformatics (http://www.gdch.de/gcc2008) to be held = in Goslar, Germany, November 9 - 11, 2008. The conference program is now online: = http://www.gdch.de/vas/tagungen/tg/5327/scientific__e.htm Because of the strong increase of the number of attendees during the = last two conferences, we have to impose a limit for the number of = conference participants this year (200 max).=20 Please register as early as possible. Until now we have already more = than 130 participants!=20 You will find the online registration here: = http://www.gdch.de/vas/tagungen/tg/5327/anmeld__e.htm Please remember to book also a hotel room in the conference hotel 'Der = Achtermann', keyword "CIC 2008" The specific conference offer will end on October 9, 2008. There will be two free software workshops right before the conference = opening on Sunday afternoon. CCG will offer a tutorial session = introducing new features of the 2008 release of MOE and Xemistry will = offer a tutorial introducing the scripting capabilities of the chemical = information processing toolkit CACTVS. Visit the conference website at www.gdch.de/gcc2008 for more = information. Invited Speakers are: J=FCrgen Bajorath, University of Bonn, D Michael Berthold, University of Konstanz , D=20 Marcus Elstner, University of Braunschweig, D=20 Robert Glen, Cambridge University, UK=20 Kurt Varmuza, Technical University of Vienna, A=20 Steve M. Bachrach, Trinity University, TX, USA I hope to see you in Goslar. Frank Oellien, Conference Chairman Mit freundlichen Gr=FC=DFen / With kind regards=20 Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien^sp.intervet.com Phone: +49 (6130) 948 365 =09 Fax: +49 (6130) 948 517 =09 =20 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From owner-chemistry@ccl.net Mon Sep 29 11:34:00 2008 From: "Mario Citra citra],[syrres.com" To: CCL Subject: CCL: software for predicting chemical environmental fate Message-Id: <-37819-080929111859-27119-bnBpSQAMm6G0KeDIeSZD9Q[]server.ccl.net> X-Original-From: "Mario Citra" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 29 Sep 2008 10:19:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Mario Citra" [citra!A!syrres.com] For a good review of the fugacity models see: Mackay D, Paterson S, Shiu WY (1992) Generic models for evaluating the regional fate of chemicals. Chemosphere 24 : 695-718. Don Mackays group has lots of free software regarding this subject. http://www.trentu.ca/academic/aminss/envmodel/welcome.html There are some on-lie versions of these programs developed for somewhat specific applications. One for screening chemicals in the Great Lakes: http://glad.syrres.com/default.asp one for estimating persistence toxicity and bioaccumulation: http://www.pbtprofiler.net/ -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] Sent: Saturday, September 27, 2008 4:38 PM To: Citra, Mario J. Subject: CCL: software for predicting chemical environmental fate Sent to CCL by: "Chunhui Li" [baotogo2004]|[gmail.com] Dear All: I am looking for software (either free or not) which can predict the chemical partition between different compartments in the environment. All I know so far is the EPIWIN fugacity model. and also, I really appreciate if anyone can point me some nice review papers about these models. Thanks in advance! Lilyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt