From chemistry-request@server.ccl.net Sun Jun 6 06:00:24 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23001 for ; Sun, 6 Jun 1999 06:00:23 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA52228; Sun, 6 Jun 1999 11:58:10 +0200 (CEST) Date: Sun, 6 Jun 1999 11:58:10 +0200 From: Christian Pilger To: maoxiang cc: chemistry@ccl.net Subject: Re: CCL:question about autodock In-Reply-To: <37588DC9.167E@iris.sipp.ac.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 5 Jun 1999, maoxiang wrote: > Hi, everyone: > I am an new man in the CCL. > Here is a question I wish you can help me. I am using AUTODOCK(ver > 2.4) to dock my ligand, but I find almost all of the result of the > position of ligand have bumps with the receptor. Does someone have met > the problem in the work, maybe there are some mistakes in my setup. Hope > to hear from you soon. > > > With best regards, > Mao Xiang > Dear Mao Xiang, we obtained similar results with AutoDock. I think one cause may be the grid-spacing you enter into AutoGrid (by default: 0.375 A). If you decreased the distance between the grid points I would expect you to get better energies and less bumbs. However to overcome this problem and at the same time the problem of receptor rigidity we used a different force field (i.e. TRIPOS) to achive some "fine-tuning" of the ligand-enzyme- alignments suggested by AutoDock. The applied force field distinguished more atom types than AutoDock does and additionally allowed us to keep those amino acid residues flexible, that were flanking our proposed binding site ("induced fit"). Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de Word Wide Web: http://oc30.uni-paderborn.de/~cpilger ----------------------------------------------------------------- From chemistry-request@server.ccl.net Sun Jun 6 12:23:08 1999 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA17763 for ; Sun, 6 Jun 1999 12:23:06 -0400 Received: from localhost by dedalus.lcc.ufmg.br (AIX 3.2/UCB 5.64/4.03) id AA41021; Sun, 6 Jun 1999 13:17:04 -0300 Organization: Universidade Federal de Minas Gerais - LCC - Brasil Date: Sun, 6 Jun 1999 13:17:04 -0300 (BSC) From: andre mauricio de oliveira To: Yantao Chen Cc: chemistry@ccl.net Subject: Re: CCL:3D QSAR In-Reply-To: <3.0.32.19990604173417.0069329c@159.226.86.106> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dr Chen, Program Sybyl (www.tripos.com) can perform CoMFA calculations. There is a book by Dr Hugo Kubyini reporting 3D-QSAR. Best regards. On Fri, 4 Jun 1999, Yantao Chen wrote: > Dear Sirs: > > I am trying to find some useful information on 3D QSAR study, especially > its application in drug design and synthesis. I also want to know the > popular softwares utilized in lab. If you can mail me the related materials > I will greatly appreciate. > > Thanks a lot. > > Yantao Chen > > > ********************************** > Yantao Chen, Ph. D. > Group 507, Institute of Chemistry > Chinese Academy of Sciences > P.O. Box 2709, Beijing 100080 > P. R. China > > Fax: +86-10-62559373 > Email: ychen@pplas.icas.ac.cn > ********************************** > -= 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 > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@server.ccl.net Sun Jun 6 02:16:31 1999 Received: from grebe.prod.itd.earthlink.net (grebe.prod.itd.earthlink.net [207.217.120.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA20960 for ; Sun, 6 Jun 1999 02:16:30 -0400 Received: from lrz.de (1Cust162.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.162]) by grebe.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id XAA10248; Sat, 5 Jun 1999 23:10:53 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id XAA12240; Sat, 5 Jun 1999 23:08:05 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Sat, 5 Jun 1999 23:08:04 -0700 (PDT) To: , nsg-d@world.std.com Cc: CHMINF-L@LISTSERV.INDIANA.EDU Subject: SUMMARY: SMILES query X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <14170.251.570937.387552@lrz.de> This is the summary of the answers I got for my query on resources for (U)SMILES ( http://www.daylight.com/dayhtml/doc/theory/theory.toc.html ) generation and manipulation. It seems that interim Daylight has silently revised the USMILES (unique SMILES) specs so that currently (1999) ~30% of the free NCI database now differs if compared to those produced using the rules >from the original (1989) publication. Hopefully, in near future either the new specs will be published or the generation algorithm reverse- engineered. Thanks to all who contributed. Regards, Eugene Leitl Edited replies follow. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: Peter Bladon I have written software for _parsing_ SMILES strings as a means of structure input to the INTERCHEM modelling system, and as a general way of generating 3D-structural data. I have not undertaken the generation of unique SMILES strings, although I am actively considering it. The version of SMILES I have adopted is the simple one outlined in the original papers by the Weiningers. But I have adapted it to take care of conformational and chirality information to simplify the generation of 3D-structures. So the chirality information is specified in a different way to that used in the current Daylight codes. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: Nick Jewell I use Tripos's dbtranslate facility (comes with the Unity database package) to convert smiles into MOL or MOL2 formats. All in all, similar to babel but more helpfully documented. For more information on this source, consult http://www.tripos.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: Ferenc Csizmadia Marvin Sketch generates SMILES and SMARTS (an extension of SMILES for querying) strings and other formats. See http://www.chemaxon.com/marvin/ for more. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: "Wolf-Dietrich Ihlenfeldt" The CACTVS toolkit does it, too. http://www2.ccc.uni-erlangen.de/cactvs/ See also our selection of Internet chemistry services at http://www2.ccc.uni-erlangen.de/services, which generally accept SMILES as input. Other programs with SMILES capabilities: CS ChemDraw, ChemAxon Marvin Java Editor, Novartis JME Java Editor ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: alberto.gobbi@cp.Novartis.com we are using smiles extensively in our chemical databases (daylight, ORACLE) as a key for fullstructure search. There are also a few other Chemical Editors which can create SMILES: Daylight has one, there is a free one from Peter Ertl: http://www.daylight.com/bernd-cgi/Novartis/download.cgi ChemDraw others. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: "Pierre-Jean L'Heureux" MOE, a Chemical Computing Group software, does use SMILE for database searching. http://www.chemcomp.com/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Sun Jun 6 19:58:39 1999 Received: from yowie.cc.uq.edu.au (root@yowie.cc.uq.edu.au [130.102.2.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA21057 for ; Sun, 6 Jun 1999 19:58:36 -0400 Received: from avgas.ddd.uq.oz.au (avgas.ddd.uq.edu.au [130.102.118.39]) by yowie.cc.uq.edu.au (8.9.3/8.9.3) with SMTP id JAA02666 for ; Mon, 7 Jun 1999 09:52:50 +1000 (GMT+1000) Sender: dooley@yowie.cc.uq.edu.au Message-ID: <375C22EA.794B@mailbox.uq.edu.au> Date: Mon, 07 Jun 1999 09:52:10 -1000 From: Michael Dooley X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Molecular Modelling 99 Conference Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The 5th Annual Molecular Modelling 99 Conference Call for papers **Note an error in the previous URL- the correct URL** http://www.uq.edu.au/~ddmdoole/mm99 September 21-24 1999 Bardon Conference Centre, Brisbane, Australia. The Centre for Drug Design and Development and The University of Queensland are pleased to host MM99. We are seeking abstracts for papers and posters in any area of molecular modelling, with some current themes listed below. * Bioinformatics * Chemoinformatics and molecular similarity * de novo drug design * Scoring functions and QSAR * Protein-protein interactions * Material sciences For more information, please visit our web-site http://www.uq.edu.au/~ddmdoole/mm99 or contact me at m.dooley@mailbox.uq.edu.au with your mailing address and I will forward to you the conference brochure. -- ################################################################# Dr Michael Dooley Centre for Drug Design and Development The University of Queensland St Lucia, Qld, 4072 Australia Brisbane Molecular Modeling Group http://www.uq.edu.au/~ddmdoole/