From owner-chemistry@ccl.net Wed Jan 21 08:57:01 2009 From: "=?ISO-8859-2?Q?=A9imon_Budz=E1k?= budzak#fpv.umb.sk" To: CCL Subject: CCL: Decriptors for whole database Message-Id: <-38471-090121085307-25166-3+lmdPsRxMn3gmRN1H1Zeg,server.ccl.net> X-Original-From: =?ISO-8859-2?Q?=A9imon_Budz=E1k?= Content-Type: multipart/mixed; boundary="------------020109060100010306000606" Date: Wed, 21 Jan 2009 14:09:28 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-2?Q?=A9imon_Budz=E1k?= [budzak(_)fpv.umb.sk] This is a multi-part message in MIME format. --------------020109060100010306000606 Content-Type: text/plain; charset=ISO-8859-2; format=flowed Content-Transfer-Encoding: 7bit Hello, I compute some molecular descriptors in Marwin (JChem). I would like to compute those molecular descriptors for all molecules in one time and non compute molecular desciptors for each mlecule separately. How can I do this? Or if you have some another idea, which free software(or software with academic free licence) can I use? (my database includes 1285 molecules) Thank you Simon --------------020109060100010306000606 Content-Type: text/x-vcard; charset=utf-8; name="budzak.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="budzak.vcf" begin:vcard fn;quoted-printable:=C5=A0imon Budz=C3=A1k n;quoted-printable;quoted-printable:Budz=C3=A1k;=C5=A0imon org:Faculty of Natural Science, Matej Bel University ;Department of Chemistry adr;quoted-printable;quoted-printable;dom:;;Tajovsk=C3=A9ho 40;Bansk=C3=A1 Bystica;Slovakia;974 01 email;internet:budzak/a\fpv.umb.sk tel;work:+421 48 466 7210 tel;cell:+421 904 381 329 x-mozilla-html:TRUE version:2.1 end:vcard --------------020109060100010306000606-- From owner-chemistry@ccl.net Wed Jan 21 09:33:00 2009 From: "Tim Cheeseright tim#,#cresset-bmd.com" To: CCL Subject: CCL: Cresset Launches FieldStere - A bioisostere search product Message-Id: <-38472-090121055628-25636-mT2SG0ARrEoTw3dafbMDGA|a|server.ccl.net> X-Original-From: "Tim Cheeseright" Date: Wed, 21 Jan 2009 05:56:23 -0500 Sent to CCL by: "Tim Cheeseright" [tim-#-cresset-bmd.com] Cresset BMD launches FieldStere, a smart, easy to use new product that generates non-obvious drug candidates. With FieldStere, the modeller or chemist can load in a molecule, select part of it, and obtain multiple suggested bioisisteric replacements. The results are ranked according to both shape similarity and electrostatic similarity assessed over the entire molecule, not just the replaced fragment. In pre-launch testing with existing biotech and pharmaceutical customers, FieldStere performed outstandingly well and received very positive feedback. Users reported that the product consistently identified both known bioisosteres and structurally diverse but chemically intriguing compounds. For more information contact sales*|*cresset-bmd.com +44 1707 356 120 or see http://www.cresset-bmd.com/fieldstere.shtml Tim Cheeseright (tim*|*cresset-bmd.com) Cresset BMD From owner-chemistry@ccl.net Wed Jan 21 11:30:00 2009 From: "Vincenzo Verdolino vincenzo.verdolino{=}nemo.unipr.it" To: CCL Subject: CCL: energy of H+ Message-Id: <-38473-090120111816-6478-LNBPO+x0kV1NEhcZECI74g[*]server.ccl.net> X-Original-From: "Vincenzo Verdolino" Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 20 Jan 2009 16:35:45 +0100 MIME-Version: 1.0 Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino^^nemo.unipr.it] Dear, be very careful with protonation chemical processes. I didn't follow you complete discussion but I suggest to take a look at a recent paper that we published J Phys Chem B. 2008 Dec 25;112(51):16860-73 Vincenzo Verdolino On Tue, 20 Jan 2009 13:09:07 +0200, Serge Dom serge.dom[a]gmail.com wrote > Thank you for your answer. > If energy of H+ is zero I need only calculate pyridine-h and > pyridine (-) in order to calculate difference in energy between > product and reactant. Pyridine-h (0,2) has total energy -248.8282688 > au at PW91/cc-pVTZ level and pyridine (-) (-1,2) has energy - > 248.2369938. So elimination of the proton from pyridine-h molecule > is not thermodynamically favorable. Is it correct? > > Serge -- Universita' degli Studi di Parma (http://www.unipr.it) From owner-chemistry@ccl.net Wed Jan 21 12:04:01 2009 From: "Wolf-D. Ihlenfeldt wdi ~~ xemistry.com" To: CCL Subject: CCL: Decriptors for whole database Message-Id: <-38474-090121112816-7969-yFp4oqOFGPa1RbDFWoey0A_+_server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="ISO-8859-2" Date: Wed, 21 Jan 2009 16:38:44 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi]~[xemistry.com] W. D. Ihlenfeldt Xemistry GmbH wdi##xemistry.com --- xemistry gmbh - Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > -----Original Message----- > From: owner-chemistry+wdi=3D=3Dxemistry.com##ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com##ccl.net] On Behalf Of =A9imon Budz=E1k > budzak#fpv.umb.sk > Sent: Wednesday, January 21, 2009 2:09 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: Decriptors for whole database >=20 > Hello, >=20 > I compute some molecular descriptors in Marwin (JChem). Which descriptors are these? I would like to > compute those molecular descriptors for all molecules in one time and > non compute molecular desciptors for each mlecule separately. How can = I > do this? Or if you have some another idea, which free software(or > software with academic free licence) can I use? (my database includes > 1285 molecules) This has not yet been officially released, but the 3.356 version of the CACTVS toolkit includes, implemented in a collaborative effort of the = groups of Huixiao Hong, National Center for Toxicological Research, US FDA; = Mark Nicklaus, LMCh, NCI; and Xemistry GmbH, a complete MOLD2 descriptor = module, which computes 777 (!) well-known structure descriptors from literature. = Cactvs is a multi-platform scriptable chemical information processing toolkit which can read and write a large number of exchange file format = for structures, reactions, tables etc. It is straightforward to set up a = small processing script to go through your database in one run. The software = is free for academic use. If you tell me your platform, I will make available a pre-release = package for you, and also help you with setting up your processing script. Regards From owner-chemistry@ccl.net Wed Jan 21 12:56:00 2009 From: "Bikadi Zsolt zsolt.bikadi .. virtuadrug.com" To: CCL Subject: CCL: Decriptors for whole database Message-Id: <-38475-090121125519-29204-E+3cQ6fhyu5EtGHTo3uCfg]=[server.ccl.net> X-Original-From: "Bikadi Zsolt" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-2" Date: Wed, 21 Jan 2009 18:55:03 +0100 MIME-Version: 1.0 Sent to CCL by: "Bikadi Zsolt" [zsolt.bikadi{}virtuadrug.com] Hello, You can calculate descriptors in command mode of Marvin for all = molecules using the cxcalc command in a DOS/Unix prompt. You can also check out Pclient server for these type of calculations. Zsolt Zsolt Bikadi, PhD DockingServer Team =20 -----Original Message----- > From: owner-chemistry+zsolt.bikadi=3D=3Dvirtuadrug.com]-[ccl.net [mailto:owner-chemistry+zsolt.bikadi=3D=3Dvirtuadrug.com]-[ccl.net] On = Behalf Of =A9imon Budz=E1k budzak#fpv.umb.sk Sent: Wednesday, January 21, 2009 2:09 PM To: Bikadi, Zsolt Subject: CCL: Decriptors for whole database Hello, I compute some molecular descriptors in Marwin (JChem). I would like to compute those molecular descriptors for all molecules in one time and = non compute molecular desciptors for each mlecule separately. How can I do = this? Or if you have some another idea, which free software(or software with academic free licence) can I use? (my database includes 1285 molecules) Thank you Simon From owner-chemistry@ccl.net Wed Jan 21 15:48:00 2009 From: "Phil Payne ppayne,+,aryx.com" To: CCL Subject: CCL: Induced Fit docking: Schrodinger Message-Id: <-38476-090121150645-7236-vKz3Avc1cNLPw7f9I58+OQ[-]server.ccl.net> X-Original-From: "Phil Payne" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C97BFF.3C706BFC" Date: Wed, 21 Jan 2009 11:34:11 -0800 MIME-Version: 1.0 Sent to CCL by: "Phil Payne" [ppayne[a]aryx.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C97BFF.3C706BFC Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Mr. Sharma - =20 I have done many Schrodinger IFD calculations. What is your question? =20 - Phil Payne, Sr. Scientist, Aryx Therapeutics =20 ________________________________ > From: owner-chemistry+ppayne=3D=3Daryx.com()ccl.net [mailto:owner-chemistry+ppayne=3D=3Daryx.com()ccl.net] On Behalf Of = hirdesh kumar hirdeshs8*gmail.com Sent: Friday, January 16, 2009 10:17 PM To: Phil Payne Subject: CCL: Induced Fit docking: Schrodinger =20 Hi All; I am troubling with Induced fit docking module of schrodinger. Is there anyone familiar with this module --=20 Hirdesh Kumar Sharma M.S. 4th Semester A-212; Educational Block Center for Pharmacoinformatics NIPER, Sector 67, S.A.S. Nagar, Mohali Punjab-160062 ------_=_NextPart_001_01C97BFF.3C706BFC Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Mr. Sharma = –

 

I have done many Schrodinger IFD calculations.  What is your question?

 

- Phil = Payne, Sr. Scientist, Aryx Therapeutics

 

From: owner-chemistry+ppayne=3D=3Daryx.com()ccl.net [mailto:owner-chemistry+ppayne=3D=3Daryx.com()ccl.net] On Behalf Of hirdesh kumar hirdeshs8*gmail.com
Sent: Friday, January 16, = 2009 10:17 PM
To: Phil Payne
Subject: CCL: Induced Fit = docking: Schrodinger

 

Hi All;
I am troubling with Induced fit docking module of schrodinger. Is there = anyone familiar with this module

--
Hirdesh Kumar Sharma
M.S. 4th Semester
A-212; Educational Block
Center for Pharmacoinformatics
NIPER,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062

------_=_NextPart_001_01C97BFF.3C706BFC-- From owner-chemistry@ccl.net Wed Jan 21 16:58:01 2009 From: "Dave Winkler dave.winkler]=[csiro.au" To: CCL Subject: CCL: descriptors for peptides Message-Id: <-38477-090120181752-12640-taquGaRCuZgQZdOp2wtNPA : server.ccl.net> X-Original-From: Dave Winkler Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 21 Jan 2009 09:35:36 +1100 MIME-Version: 1.0 Sent to CCL by: Dave Winkler [dave.winkler:csiro.au] There are quite a few, and sometimes quite simply ones work well. Here is a reference to one of our papers that illustrate one method. Predictive Bayesian Neural Network Models of MHC Class II Peptide Binding, Burden, FR, Winkler, DA, J. Mol. Graph. Mod. 23 481-489 (2005). >Sent to CCL by: "atul agarwal" [aagarwal .. achillion.com] >Hi, > >Are there any 2D and 3D descriptors available for peptides? >References of their application and availability for pharma will be >highly appreciated. > >thanks! >Atul-- Cheers, Dave Dr. David A. Winkler FRACI CChem CPChem Email: dave.winkler-x-csiro.au Biomaterials & Regenerative Medicine Voice: 61-3-9545-2477 Senior Principal Research Scientist Fax: 61-3-9545-2561 CSIRO Molecular and Health Technologies or 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au http://www.csiro.au/csiro/content/standard/ps1gn,,.html or http://www.wark.csiro.au/winkler/Welcome.html Join us at the 7th International Medicinal Chemistry Symposium (AIMECS09) Aug 23-27, 2009, Cairns/Great Barrier Reef, Queensland, Australia http://www.aimecs09.org/ From owner-chemistry@ccl.net Wed Jan 21 17:59:00 2009 From: "anjan roy aroy25-*-gmail.com" To: CCL Subject: CCL:G: gaussian optimization in presence of electromagetic field Message-Id: <-38478-090121175749-7707-HMXrxJ2fZMORFvJNPL+Uyw(~)server.ccl.net> X-Original-From: "anjan roy" Date: Wed, 21 Jan 2009 17:57:45 -0500 Sent to CCL by: "anjan roy" [aroy25__gmail.com] hi, I would like to know if its possible to do a DFT calculation in the presence of an external microwave ( or any other RF) radiation in gaussian03.If so is it possible to do it in the presence of some solvation? thank you Anjan