From chemistry-request@server.ccl.net Tue Jul 13 02:34:40 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA29151 for ; Tue, 13 Jul 1999 02:34:39 -0400 Received: from auric.chem.csiro.au (auric.chem.CSIRO.AU [138.194.44.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id CAA08233 for ; Tue, 13 Jul 1999 02:28:02 -0400 (EDT) Received: by auric.chem.csiro.au id AA29428 (5.67b/IDA-1.5 for chemistry@ccl.net); Tue, 13 Jul 1999 16:27:43 +1000 Received: from cpr-46107.chem.csiro.au(138.194.46.107), claiming to be "[138.194.46.107]" via SMTP by auric.chem.CSIRO.AU, id smtpd29422aaa; Tue Jul 13 06:27:37 1999 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 Jul 1999 16:27:30 +1000 To: chemistry@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU From: "Dr. Dave Winkler" Subject: Symposium on computational drug design at the 8th Asian Chemical Congress, Taipei SYMPOSIUM ON COMPUTATIONAL DRUG DESIGN AND INFORMATICS 8TH ASIAN CHEMICAL CONGRESS TAIPEI November 21-24, 1999 Taipei International Convention Center A one-day symposium will be held as part of the 8ACC (the main Congress of the Federation of Asian Chemical Societies) and will be organized by the Chemical Information Network Project (ChIN see URL: http://chin.icm.ac.cn/). The Symposium will cover any aspect of computational drug design and discovery. Details of the 8ACC can be found at the following URL: http://www.itri.org.tw/8ACC/). Call for papers. ---------------- Please contact either of the ChIN co-directors below with title of your paper as soon as possible. Dr. Dave Winkler, CSIRO Molecular Science, Private Bag 10, Clayton South MDC 3169, Australia. Phone: +61-3-9545-2477 Fax: +61-3-9545-2446 Email: dave.winkler@molsci.csiro.au Dr. Xiaoxia Li, Laboratory of Computer Chemistry, Institute of Chemical Metallurgy, Chinese Academy of Sciences, Beijing 100080 Phone: 86-10-62554066 Fax: 86-10-62561822 Email: xxia@lcc.icm.ac.cn We look forward to meeting you in Taipei. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@server.ccl.net Tue Jul 13 12:31:59 1999 Received: from carrier2.pharmacy.ohio-state.edu (carrier2.pharmacy.ohio-state.edu [128.146.80.224]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA02733 for ; Tue, 13 Jul 1999 12:31:59 -0400 Received: from carrier2.pharmacy.ohio-state.edu (localhost [127.0.0.1]) by carrier2.pharmacy.ohio-state.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA01395 for ; Tue, 13 Jul 1999 12:25:24 -0400 Sender: helsper@carrier2.pharmacy.ohio-state.edu Message-ID: <378B6873.872EB196@carrier2.pharmacy.ohio-state.edu> Date: Tue, 13 Jul 1999 12:25:23 -0400 From: Freek Helsper X-Mailer: Mozilla 4.51 [en] (X11; U; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: autodock 3.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'm trying to run Autodock to find a putative binding site in a model I've just finished. When I analyze the docking logfile (dlg-file), I only get the coordinates of the docked ligand in pdb-format. How can I view the complex of the ligand with the macromolecule (I don't have AVS, so that's not an option). There's nothing about this in the Autodock manual. Has anyone an idea how to solve this problem? Freek Helsper -- ##################################################################### Freek Helsper Tel:+1 614 292 9646 College of Pharmacy Fax:+1 614 292 9977 The Ohio-State University Parks Hall, room 357 500 W 12th Ave Columbus, OH 43210 http://carrier2.pharmacy.ohio-state.edu/~helsper/Public/homepage.html ##################################################################### From chemistry-request@server.ccl.net Tue Jul 13 13:39:37 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA03856 for ; Tue, 13 Jul 1999 13:39:36 -0400 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay1.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id KAA13984; Tue, 13 Jul 1999 10:32:59 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by elvis.scripps.edu (8.9.2/TSRI-3.0) with ESMTP id KAA57056; Tue, 13 Jul 1999 10:32:59 -0700 (PDT) Sender: yadavm@scripps.edu Message-ID: <378B784A.C0CB3D0B@scripps.edu> Date: Tue, 13 Jul 1999 10:32:58 -0700 From: Maneesh Yadav X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Freek Helsper , CHEMISTRY@ccl.net Subject: Re: CCL:autodock 3.0 References: <378B6873.872EB196@carrier2.pharmacy.ohio-state.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit When some modellers load up multiple molecules, they sometimes apply wierd transforms so you can't see the true docked complex (insightII). Use a modeller like SPOCK and load up the macromolecule and ligand and it gives you no problems. Freek Helsper wrote: > I'm trying to run Autodock to find a putative binding site in a model > I've just finished. > When I analyze the docking logfile (dlg-file), I only get the > coordinates of the docked ligand in pdb-format. How can I view the > complex of the ligand with the macromolecule (I don't have AVS, so > that's not an option). There's nothing about this in the Autodock > manual. > Has anyone an idea how to solve this problem? > > Freek Helsper > > -- > ##################################################################### > Freek Helsper Tel:+1 614 292 9646 > College of Pharmacy Fax:+1 614 292 9977 > The Ohio-State University > Parks Hall, room 357 > 500 W 12th Ave > Columbus, OH 43210 > > http://carrier2.pharmacy.ohio-state.edu/~helsper/Public/homepage.html > ##################################################################### > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Jul 13 18:28:46 1999 Received: from stork.EMBL-Heidelberg.DE (stork.EMBL-Heidelberg.DE [192.54.41.54]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA06276 for ; Tue, 13 Jul 1999 18:28:34 -0400 Received: from jay.EMBL-Heidelberg.DE (jay.EMBL-Heidelberg.DE [192.54.41.153]) by stork.EMBL-Heidelberg.DE (8.8.4/8.8.4) with SMTP id AAA25118; Wed, 14 Jul 1999 00:21:51 +0200 (MDT) Date: Wed, 14 Jul 1999 00:21:51 +0200 (MDT) From: "Rebecca C. Wade" Reply-To: "Rebecca C. Wade" To: CHEMISTRY@ccl.net cc: Rebecca Wade , Razif Gabdoulline Subject: Java molecule viewer : MolSurfer Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ********* MolSurfer ********* Following the CCL discussion on Java 3D molecular viewers, we would like to announce the release of a new Java-based molecular interaction visualization and analysis software, MolSurfer, available from our webserver and to download (see: http://www.embl-heidelberg.de/ExternalInfo/wade/pub/soft/molsurfer.html). This software is a graphical tool for studying protein-protein interfaces. It links a 2D projection of a protein-protein interface to a 3D view of the protein structures. This Java-based software uses the representation of the protein- protein interface generated by ADSI, the interface-mapping module of ADS (analytically defined surfaces) software [1], and WebMol, a Java-based PDB viewer [2]. It is described in this month's issue of TIBS [3]. Please try out MolSurfer. All feedback appreciated. Razif Gabdoulline, Rebecca Wade & Dirk Walter European Molecular Biology Laboratory, Heidelberg Refs: [1] R.R.Gabdoulline & R.C.Wade (1996) J.Mol.Graph. 14, 341-353. [2] D.Walther (1997) Trends Biochem.Sci. 22, 274-275. [3] R.R.Gabdoulline, R.C.Wade & D.Walther (1999) Trends Biochem.Sci. 24, 285-287. ----------------------------------------------------------------------- Rebecca Wade Internet Wade@EMBL-Heidelberg.DE Address EMBL, Meyerhofstr 1, 69117 Heidelberg, Germany Tel +49 (0)6221 387553, Fax +49 (0)6221 387517 URL http://WWW.EMBL-Heidelberg.DE/~wade/ -----------------------------------------------------------------------