From owner-chemistry@ccl.net Tue Dec 20 08:36:00 2005 From: "Madhusudhan n bioinfo.msn=gmail.com" To: CCL Subject: CCL: what r the steps in the creation of a software 4 toxicity prediction of ligands Message-Id: <-30368-051220031951-7794-B41A/HRoA/t7CfDdgJ9gBA]_[server.ccl.net> X-Original-From: Madhusudhan n Content-Type: multipart/alternative; boundary="----=_Part_2894_8436972.1135063045324" Date: Tue, 20 Dec 2005 12:47:25 +0530 MIME-Version: 1.0 Sent to CCL by: Madhusudhan n [bioinfo.msn#%#gmail.com] ------=_Part_2894_8436972.1135063045324 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline > > dear friends, > i am working in a small company, which want 2 create a software 4 toxicit= y > prediction of ligands & drugs. in this process they want 2 design a toxic chemicals DB pl help by telling how 2 proceed in the project(toxicity prediction) . can i use neural networks or alternative mapping methods like recursive partitioning or SVM. pl. convey the message to all in the group. if u know any specific discussion groups,which can help me,pl.farward the list,i will ask their help. i hope u can help me to come out of this trouble in project.the project is about designing a software4 toxicity prediction. i am eargerly waiting 4 instructions from u, by madhusudhan bioinfo.msn|at|gmail.com ------=_Part_2894_8436972.1135063045324 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
dear friends,
i am worki= ng in a small company, which want 2 create a software 4 toxi= city prediction of ligands & drugs.
 
in this process they want 2 design a toxic chemicals DB 
 
pl help by telling how 2 proceed in the project(toxicity prediction) .=
can i use neural networks or alternative mapping methods like recursive= partitioning or SVM.
pl. convey the message to all in the group.
if u know any specific discussion groups,which can help me,pl.farward the l= ist,i will ask their help.
i hope u can help me to come out of this trou= ble in project.the project is about designing a software4 toxicity predicti= on.=20
i am eargerly waiting 4 instructions from u,
by
madhusudhan
bioinfo.msn|at|gmail.com
 
------=_Part_2894_8436972.1135063045324-- From owner-chemistry@ccl.net Tue Dec 20 13:54:01 2005 From: "Kim Branson kim.branson{}gmail.com" To: CCL Subject: CCL: HTS Screen Summary Message-Id: <-30369-051220134800-22453-o4nbYA0nWvi7CkPbTWzmMw * server.ccl.net> X-Original-From: Kim Branson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 20 Dec 2005 08:29:05 -0800 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Kim Branson [kim.branson[-]gmail.com] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all Here is a summary of the responses i have received for public HTS data resources.: Based on the responses I have received, and the data i have found, there are very few public sources of information The McMasters HTS library has 2 sets, SARS protease, and the DHFR set. The harvard screening facility have data for numerous screens, some which have known xray structures associated with them. Accessing the structures of the compounds used in the screen is difficult. One cannot simply download the structures, (unless you write a automated web request program.. ) The set of CDK-2 ligands in http://dx.doi.org/10.1021/jm020472j responses below. cheers Kim ________________________________________________________________________ _______ Responses Below: Sent to CCL by: "Michael K. Gilson" BindingDB now allows SDfile downloads of compounds and inhibition constants for a given target. I'm not sure if this is exactly what you are after, though, since these are not HTS sets. On the other hand, some targets have hundreds of compounds. You might also want to look at what is available now at PubChem. Regards, Mike Sent to CCL by: Greg Landrum Though it's not exactly HTS data, a large quantity of data about CDK2 ligands is available in the supplementary material associated with this paper: Bradley, E. K.; Miller, J. L.; Saiah, E.; Grootenhuis, P. D. Informative library design as an efficient strategy to identify and optimize leads: application to cyclin-dependent kinase 2 antagonists. J Med Chem 2003, 46, 4360-4364. http://dx.doi.org/10.1021/jm020472j The authors screened ~16K compounds for CDK2 activity and report all the results. Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi%a%xemistry.com] I suggest you look at PubChem (pubchem.ncbi.nlm.nih.gov). W. D. Ihlenfeldt Xemistry GmbH wdi..xemistry.com Kim, You also might want to check the HTS group at McMaster University in Hamilton. They sponsored a competition on HTS data mining this past year. The web site can be found at http://hts.mcmaster.ca/HTSDataMiningCompetition.htm . The data set was entirely based on DHFR inhibition, but it included several novel inhibitors and the results of the screens they used as the basis of the competition are now in the literature. Hopefully this will be a regular sort of contest from various research groups and we will be able to get a "bake-off" of methods in virtual screening and HTS analysis going on a regular basis. Andy Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 kbranson,,svi.edu.au kim.branson,,gmail.com www.svi.edu.au "Reminds me of the time I went to Africa, someone forgot the corkscrew and we had to live on food and water for days." W.C. Fields -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) iD8DBQFDqDFR3QNu8KNs0LgRApm0AKCFqopdsUP9kYnlflzKm/8ysRfxwgCfdspJ nUhOV+3HDgErYOeNmNmcq7E= =sHKb -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Tue Dec 20 20:31:00 2005 From: "Vladimir Pitchko vladimir.pitchko:_:concordia.ab.ca" To: CCL Subject: CCL:G: Gaussian 03 on Debian 3.1 Message-Id: <-30370-051220184539-32238-zFSMSXi5lueLT8kpUE89Cw*o*server.ccl.net> X-Original-From: "Vladimir Pitchko" Sent to CCL by: "Vladimir Pitchko" [vladimir.pitchko,+,concordia.ab.ca] I want to try Gaussian 03 on Pentium with Debian GNU/Linus 3.1. Does somebody have experience with that? From owner-chemistry@ccl.net Tue Dec 20 21:06:01 2005 From: "wbx wangbx[A]dicp.ac.cn" To: CCL Subject: CCL:G: install G03 in linux Message-Id: <-30371-051220201520-7327-hrmmbXRfx/3bOCTzZxpLYQ_+_server.ccl.net> X-Original-From: "wbx" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Wed, 21 Dec 2005 09:15:13 +0800 Mime-Version: 1.0 Sent to CCL by: "wbx" [wangbx**dicp.ac.cn] Dear All£¬ now i am going to install G03 in linux. though i try many times, it still doesn't work. i don't know what's wrong with it. when i finish installing the G03 and run a job, it shows that it is out of the space. it seems that the environment variable isn't correctly set. while someone tell me that my linux is not suitable for the G03. my linux is Fedora core 3. please let me know what's wrong and how i should do. thank you very much! Any advice is useful!! With best regards, sincerely, Bingxing Wang 2005-12-21 ***************************** State Key Laboratory of Molecular Reaction Dynamics Dalian Institute of Chemical Physics Chinese Academy of Sciences Tel:086-0411-84379037 Fax:086-0411-84675584 email: wangbx-,-dicp.ac.cn