From owner-chemistry@ccl.net Fri Jan 3 07:56:00 2014 From: "N. Sukumar nagams() rpi.edu" To: CCL Subject: CCL: QSAR on MOE Message-Id: <-49506-140103064236-17666-LJgLj/7dwXr1ZdmbYo8ROw _ server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 03 Jan 2014 6:43:03 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams#rpi.edu] If you are using x3D descriptors, Yes. If you are using only 2D and i3D descriptors, No. N. Sukumar Professor of Chemistry Shiv Nadar University, India ---------------------------- "Pursue something so important that even if you fail, the world is better off with you having tried." -- Tim O'Reilly http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470769009.html ==============Original message text=============== On Tuesday, December 31, 2013 1:13 PM, Sobia Ahsan Halim sobia_halim~~yahoo.com wrote: Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim[-]yahoo.com] Hi All, I am using MOE for QSAR analysis, I just need to know do we have to align molecules before QSAR on MOE like we do on COMFA and CoMSIA or not. Thanks in advance and Happy new year Sobiathe strange characters on the top line to the ,+, sign. You can also E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or use ===========End of original message text=========== From owner-chemistry@ccl.net Fri Jan 3 10:08:01 2014 From: "Wang Jian jian.wang^-^inbox.com" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49507-140102210125-6189-hygXgos8plGKj8+PemAJ1Q,,server.ccl.net> X-Original-From: Wang Jian Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII Date: Thu, 2 Jan 2014 18:01:18 -0800 Mime-Version: 1.0 Sent to CCL by: Wang Jian [jian.wang_._inbox.com] <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22> Hi, happy new year=21

Can anyone recommend some free software for = conformation analysis and flexible alignment of ligands onto a bioactive = conformation of reference (or template) molecule?

I have some = information such as ChemAxon, FieldAlign, etc. And I want to find = more.

Thanks in advance=21

Jian

3D=223D

Free 3D Marine Aquarium = Screensaver
Watch dolphins, sharks & orcas on your desktop=21 = Check it out at www.inbox.com/marineaquari= um

From owner-chemistry@ccl.net Fri Jan 3 10:43:01 2014 From: "Jian Wang jian.wang---inbox.com" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49508-140102231029-30212-dEZ8JbAsKzHKf6jXauTNHA++server.ccl.net> X-Original-From: "Jian Wang" Date: Thu, 2 Jan 2014 23:10:19 -0500 Sent to CCL by: "Jian Wang" [jian.wang(0)inbox.com] Hi, happy new year! Can anyone recommend some free software for conformation analysis and flexible alignment of ligands onto a bioactive conformation of reference (or template) molecule? I have some information such as ChemAxon, FieldAlign, etc. And I want to find more. Thanks in advance! Jian From owner-chemistry@ccl.net Fri Jan 3 12:56:00 2014 From: "Michel Petitjean petitjean.chiral^gmail.com" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49509-140103122318-21854-cQGx0Fwwm8GSjhWGszuO0g::server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=047d7b675e820c353a04ef142a5d Date: Fri, 3 Jan 2014 18:23:10 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral|,|gmail.com] --047d7b675e820c353a04ef142a5d Content-Type: text/plain; charset=ISO-8859-1 Hi, Please have a look at my softwares/freewares web page (URL below): * To align rigid conformers of the same molecule, look at ARMS and POSE. * To align rigid conformers of different molecules, look at CSR. * To align non rigid conformers, select "representative" conformers of the molecule then do a rigid alignment. * To select "representative" conformers of a molecule, generate an excess of conformers with some conformer generator (e.g. Frog2 or else) then extract the "representative" ones with DIVCF. Happy New Year ! Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral(~)gmail.com (preferred), michel.petitjean(~)univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html 2014/1/3 Wang Jian jian.wang^-^inbox.com > Sent to CCL by: Wang Jian [jian.wang_._inbox.com] > Hi, happy new year! > Can anyone recommend some free software for conformation analysis and > flexible alignment of ligands onto a bioactive conformation of reference > (or template) molecule? > I have some information such as ChemAxon, FieldAlign, etc. And I want to > find more. > Thanks in advance! > > Jian > --047d7b675e820c353a04ef142a5d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi,

Please have a look at= my softwares/freewares web page (URL below):

* To align rigid con= formers of the same molecule, look at ARMS and POSE.

* To align ri= gid conformers of different molecules, look at CSR.

* To align non rigid conformers, select "representative" co= nformers of the molecule then do a rigid alignment.

* To select "representative" conformers of a molecule,= generate an excess of conformers with some conformer generator (e.g. Frog2= or else) then extract the "representative" ones with DIVCF.

Happy New Year !

Michel.

Michel Petitjean
MTi, INSERM UMR-= S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, Fr= ance.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral(~)gmail.com (preferred),
=A0= =A0=A0=A0=A0=A0=A0 michel.petitjean(~)univ-paris-diderot.fr
h= ttp://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

<= div class=3D"gmail_extra">

2014/1/3 Wang Jian= jian.wang^-^inbox.com &= lt;owner-chemi= stry(~)ccl.net>

Sent to CCL by: Wang Jian [jian.wang_._inbox.com]
Hi, happy new year!
Can anyone recommend some free software for conform= ation analysis and flexible alignment of ligands onto a bioactive conformat= ion of reference (or template) molecule?
I have some information = such as ChemAxon, FieldAlign, etc. And I want to find more.=A0
Thanks in advance!

Jian
=

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