From chemistry-request@server.ccl.net Mon Jan 24 01:07:19 2000 Received: from hestia.its.deakin.edu.au (hestia.its.deakin.edu.au [128.184.136.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA05927 for ; Mon, 24 Jan 2000 01:07:10 -0500 Received: from [128.184.88.105] (128-184-88-105.bcs.deakin.edu.au [128.184.88.105]) by hestia.its.deakin.edu.au (Postfix) with ESMTP id DA173C385 for ; Mon, 24 Jan 2000 16:01:04 +1100 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: Date: Mon, 24 Jan 2000 14:32:02 +1000 To: computational chemistry list From: "Kieran F Lim (Lim Pak Kwan)" Subject: recommended platform for MSI insight? Content-Type: text/plain; charset="us-ascii" ; format="flowed" I am interested in purchasing Insight/Discover/Biopolymer. Right now I am at the planning and applying for funding stage. any recommendations for SGI hardware specifications to install and run Insight/Discover/Biopolymer? sincerely Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Mon Jan 24 10:31:08 2000 Received: from mailjay.creighton.edu (mailjay.creighton.edu [147.134.2.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08859 for ; Mon, 24 Jan 2000 10:31:07 -0500 From: crwatts@creighton.edu Received: from bluejay.creighton.edu (bluejay.creighton.edu [147.134.2.20]) by mailjay.creighton.edu (8.9.3 (PHNE_18979)/8.8.6) with ESMTP id IAA02831 for ; Mon, 24 Jan 2000 08:25:04 -0600 (CST) Date: Mon, 24 Jan 2000 08:24:58 -0600 (CST) To: Computational Chemistry List Subject: Dihedral Order Parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues: I'm looking for the references that describe the methodology for the calculation of backbone dihedral order parameters from molecular dynamics trajectories as well as NMR data. Regards, Charles R. Watts, Ph.D. ************************************ Research Assistant * * Department of Biomedical Sciences * An appeaser is one who feeds * Creighton University * a crocodile, hoping it will eat * School of Medicine * him last. * 2500 California Plaza * * Omaha, NE 68178 * -Winston Churchill * phone: (402) 280-2210 * * Fax: (402) 553-8841 * * E-Mail: crwatts@bluejay.creighton.edu ************************************ From chemistry-request@server.ccl.net Mon Jan 24 10:03:21 2000 Received: from petersgate.proteus.co.uk (petersgate.proteus.co.uk [195.224.44.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08762 for ; Mon, 24 Jan 2000 10:03:20 -0500 Received: from icthus.proteus.co.uk (icthus.proteus.co.uk [193.115.24.114]) by petersgate.proteus.co.uk (8.9.3/8.9.3) with ESMTP id NAA18926 for ; Mon, 24 Jan 2000 13:59:07 GMT Received: from protherics.com (WINSERV1 [193.115.24.242]) by icthus.proteus.co.uk (8.9.3/8.9.3) with ESMTP id OAA25449 for ; Mon, 24 Jan 2000 14:04:48 GMT Message-ID: <388C5981.FE8C8657@protherics.com> Date: Mon, 24 Jan 2000 13:54:10 +0000 From: Jin Li Organization: Protherics Molecular Design Ltd To: chemistry@ccl.net Subject: Molecular Docking and Virtual Screening Dear All, Protherics Molecular Design Ltd and SGI announced the completion of a collaborative project, called DockCrunch, which involved docking of over 1,000,000 molecules against two protein structures. For further details, please visit the following URLs: http://www.protherics.com/new/PRO240100.htm (or alternatively from Protherics' homepage then Investors->Press Releases) http://www.protherics.com/crunch/ Jin Li Vcard: Protherics Molecular Design Ltd Li, Jin tel-fax:(44) 1625 500666 tel-work:(44) 1625 500555 Protherics Molecular Design Ltd Jin.Li@protherics.com Head of Computational Chemistry Beechfield House Lyme Green Business Park Macclesfield Cheshire SK11 0JL, UK From chemistry-request@server.ccl.net Mon Jan 24 10:39:44 2000 Received: from linux2.ipc.pku.edu.cn (mao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA08910 for ; Mon, 24 Jan 2000 10:39:41 -0500 Received: from localhost (mao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id WAA23147; Mon, 24 Jan 2000 22:37:13 +0800 Date: Mon, 24 Jan 2000 22:37:13 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" cc: PDB List Subject: molsee 0.2 released Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all, I added a new feature into molsee: If you change display mode in molsee, molsee will reserve your display mode when you load new molecule to rasmol. ftp://mdl.ipc.pku.edu.cn/pub/software/molsee/molsee Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 From chemistry-request@server.ccl.net Mon Jan 24 15:56:52 2000 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA10392 for ; Mon, 24 Jan 2000 15:56:52 -0500 Received: from localhost (renxiao@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id MAA17350 for ; Mon, 24 Jan 2000 12:00:02 -0800 (PST) X-Authentication-Warning: neon.chem.ucla.edu: renxiao owned process doing -bs Date: Mon, 24 Jan 2000 12:00:02 -0800 (PST) From: Renxiao Wang To: Computational Chemistry List Subject: Summary: flexible docking program Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everybody! Two weeks ago we posted a message looking for a docking program that can handle the flexibility of the receptor. It seems that the answers focus on InsightII/affinity and Sybyl/FlexX. Here are the details: --------------------------------------------------------------------------- Date: Mon, 24 Jan 2000 09:55:33 +0100 From: Pieter.Stouten@eu.pnu.com (Pieter Stouten) You might want to look at Affinity from MSI (URL http://www.msi.com/life/products/insight/modules/affinity.html). It is an automatic docking module for Insight II that incorporates Monte Carlo and simulated annealing methods to place a ligand within a receptor. The method is designed so that after the Monte Carlo phase the receptor within the defined binding site is flexible by default. In other words, all you have to do is define the extent of the binding site. Every receptor atom within that region is flexible and free to move. Recent publications using Affinity are: 1. Kurinov, I. V., Myers, D. E., Irvin, J. D., Uckun, F. M. 1999. X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs. Prot. Sci. 8:1765-72 2. Read, M. A., Wood, A. A., Harrison, J. R., Gowan, S. M., Kelland, L. R., et al. 1999. Molecular Modeling Studies on G-Quadruplex Complexes of Telomerase Inhibitors: Structure-Activity Relationships. J. Med. Chem. San Diego, CA 92121 ----------------------------------------------------------------------------- Date: Mon, 17 Jan 2000 19:15:29 -0800 From: Andre de Oliveira Try FlexX available in Sybyl (www.tripos.com). (This procedure allows the user to define rotatable torsions both on ligand and receptor. It uses a genetic algorithm to sample conformations and uses force field to estimate the interaction energy.) ----------------------------------------------------------------------------- Date: Tue, 18 Jan 2000 10:12:21 -0500 From: Shaomeng Wang (Prof. Wang's group has developed a new method to perform flexible docking. But I am not sure whether the program is available now.) You may want to check out the following publications from my group. Pak, Y. and Wang, S. Application of a new molecular dynamics simulation method with a generalized effective potential to the flexible docking problems. J. Physical Chemistry,(B), 2000, 104, 354-359. Pak, Y. and Wang, S. Folding of a 16-residue helical peptide using molecular dynamics simulation with Tsallis effective potential, J. Chemical Physics, 1999, 111, 4359-4361. ----------------------------------------------------------------------------- All my best wishes, Arthur ------------------------------------------------------------------------ | Dr. Renxiao Wang | ------------------------------------------------------------------------ | Department of Chemistry and Biochemistry | 3281 Sawtelle Blvd. #104 | | University of California Los Angeles | Los Angeles, CA90066 | | Los Angeles, CA 90024 | U.S.A | | Phone: 310-8250269 (Lab) | Phone: 310-3904638 (Home) | ------------------------------------------------------------------------ | E-mail: renxiao@chem.ucla.edu | | WWW: http://zimbu.chem.ucla.edu/~arthur/ | ------------------------------------------------------------------------