From owner-chemistry@ccl.net Tue Nov 24 07:12:02 2009 From: "Gerard Pujadas gerard.pujadas:_:gmail.com" To: CCL Subject: CCL: Metabolite-structure prediction software requested Message-Id: <-40776-091124070541-7485-KCVdPvWNKxrzHwq8SOACIw- -server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0016e6d5665223f98404791cc291 Date: Tue, 24 Nov 2009 13:05:29 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas _ gmail.com] --0016e6d5665223f98404791cc291 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL list members, I would like to transform a database of drugs (for instance, in SDF format) with good ADMET properties into another database (for instance, in SDF format too) that contains the predicted structures of the most probable human metabolites of the molecules in the input file. Is there such a software? Any help will be appreciated With many thanks in advances for your help Yours sincerely Best Gerard --0016e6d5665223f98404791cc291 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL list members,

I would like to transform a database of drugs= (for instance, in SDF format) with good ADMET properties into another data= base (for instance, in SDF format too) that contains the predicted structur= es of the most probable human metabolites of the molecules in the input fil= e.

Is there such a software?

Any help will be appreciated

Wi= th many thanks in advances for your help

Yours sincerely

Best=

Gerard

--0016e6d5665223f98404791cc291-- From owner-chemistry@ccl.net Tue Nov 24 09:00:01 2009 From: "andras.borosy*givaudan.com" To: CCL Subject: CCL: Metabolite-structure prediction software requested Message-Id: <-40777-091124085633-11589-B86S2//H1WHzFDNfxZFKRQ^^^server.ccl.net> X-Original-From: andras.borosy-x-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004993B7C1257678_=" Date: Tue, 24 Nov 2009 14:23:41 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy]~[givaudan.com This is a multipart message in MIME format. --=_alternative 004993B7C1257678_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Gerard, Try SimBuilder or Metapath of OASIS: http://www.oasis-lmc.org/?section=3Dsoftware Regards, Andr=E1s Borosy "Gerard Pujadas gerard.pujadas:=5F:gmail.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com###ccl.net 24.11.2009 13:05 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Metabolite-structure prediction software requested Dear CCL list members, I would like to transform a database of drugs (for instance, in SDF=20 format) with good ADMET properties into another database (for instance, in = SDF format too) that contains the predicted structures of the most=20 probable human metabolites of the molecules in the input file. Is there such a software? Any help will be appreciated With many thanks in advances for your help Yours sincerely Best Gerard --=_alternative 004993B7C1257678_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Gerard,

Try  SimBuilder or Metapath of OASIS:

http://www.oasis-lmc.org/?section=3D= software

Regards,

Andr=E1s Borosy


"Gerard Pujadas = gerard.pujadas:=5F:gmail.com" <owner-chemistry###ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com###ccl.net

24.11.2009 13:05
Please respond to
"CCL Subscribers" <chemistry###ccl.net>
To
"Borosy, Andras " <andras.borosy###givaudan.com>
cc
Subject
CCL: Metabolite-structure prediction software requested





Dear CCL list members,

I would like to transform a database of drugs (for instance, in SDF format) with good ADMET properties into another database (for instance, in SDF format too) that contains the predicted structures of the most probable human metabolites of the molecules in the input file.

Is there such a software?

Any help will be appreciated

With many thanks in advances for your help

Yours sincerely

Best

Gerard
--=_alternative 004993B7C1257678_=-- From owner-chemistry@ccl.net Tue Nov 24 10:03:00 2009 From: "Jesus Planesas planesaj/./hotmail.com" To: CCL Subject: CCL: Metabolite-structure prediction software requested Message-Id: <-40778-091124090242-13121-qb1yJAWj7Rhgb94hGf3L3w,server.ccl.net> X-Original-From: Jesus Planesas Content-Type: multipart/alternative; boundary="_2ede9418-a89d-4587-9704-9725297d0565_" Date: Tue, 24 Nov 2009 14:29:25 +0100 MIME-Version: 1.0 Sent to CCL by: Jesus Planesas [planesaj .. hotmail.com] --_2ede9418-a89d-4587-9704-9725297d0565_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Dear Gerard =20 Test it with MOE. You can use its Database Viewer to merge 2 differents dat= abases (containing small molecules=2C protein structures=2C descriptors...)= with a common field in both to merge (id molecule...). If there is no comm= on field in your dabases you can merge also these 2 databases=2C but withou= t relation between them. =20 But it's not a free software...=20 =20 Best Regards =20 Jes=FAs =20 =20 > From: owner-chemistry-.-ccl.net To: planesaj-.-hotmail.com Subject: CCL: Metabolite-structure prediction software requested Date: Tue=2C 24 Nov 2009 13:05:29 +0100 Dear CCL list members=2C I would like to transform a database of drugs (for instance=2C in SDF forma= t) with good ADMET properties into another database (for instance=2C in SDF= format too) that contains the predicted structures of the most probable hu= man metabolites of the molecules in the input file. Is there such a software? Any help will be appreciated With many thanks in advances for your help Yours sincerely Best Gerard =20 _________________________________________________________________ Prueba algunos de los nuevos servicios en l=EDnea que te ofrece Windows Liv= e Ideas: tan nuevos que ni siquiera se han publicado oficialmente todav=EDa= . http://ideas.live.com= --_2ede9418-a89d-4587-9704-9725297d0565_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable  =3B
Dear Gerard
 =3B
Test it with MOE. You can use its Database Viewer to merge 2 differents dat= abases (containing small molecules=2C protein structures=2C descriptors...)=  =3Bwith a common field in both to merge (id molecule...). If there is = no common field in your dabases you can merge =3Balso these 2 databases= =2C but without relation between them.
 =3B
But it's not a free software...
 =3B
Best Regards
 =3B
Jes=FAs =3B =3B =3B
 =3B
> From: owner-chemistry-.-ccl.net
To: planesaj-.-hotmail.com
Subject: CCL: = Metabolite-structure prediction software requested
Date: Tue=2C 24 Nov 2= 009 13:05:29 +0100

Dear CCL list members=2C

I would like to t= ransform a database of drugs (for instance=2C in SDF format) with good ADME= T properties into another database (for instance=2C in SDF format too) that= contains the predicted structures of the most probable human metabolites o= f the molecules in the input file.

Is there such a software?

= Any help will be appreciated

With many thanks in advances for your h= elp

Yours sincerely

Best

Gerard

Prueba algunos de los nuevos servicios en l=EDnea que te ofrece Wi= ndows Live Ideas: tan nuevos que ni siquiera se han publicado oficialmente = todav=EDa. Pru=E9balo= = --_2ede9418-a89d-4587-9704-9725297d0565_-- From owner-chemistry@ccl.net Tue Nov 24 10:37:00 2009 From: "Simon Cross simon|a|moldiscovery.com" To: CCL Subject: CCL: Metabolite-structure prediction software requested Message-Id: <-40779-091124090142-12631-u3mJlqaW0h+vwaGqKTlRPA]_[server.ccl.net> X-Original-From: Simon Cross Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Nov 2009 13:08:34 +0000 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon]|[moldiscovery.com] Hi Gerard, we can this for phase I metabolism - MetaSite is predicting the metabolic hotspots with ~85% success for 9 of the human cytochromes using a combination of enzyme recognition, chemical reactivity, and mechanistic probability. These sites are then used in combination with various biotransformation reactions to predict the most likely metabolites. It is commercial software, but there is only a nominal fee for academics. You can find out more on our website (http://www.moldiscovery.com/soft_metasite.php) or contact me directly (simon [at] moldiscovery dot com) by email. Cheers, Simon Gerard Pujadas gerard.pujadas:_:gmail.com wrote: > Dear CCL list members, > > I would like to transform a database of drugs (for instance, in SDF > format) with good ADMET properties into another database (for > instance, in SDF format too) that contains the predicted structures of > the most probable human metabolites of the molecules in the input file. > > Is there such a software? > > Any help will be appreciated > > With many thanks in advances for your help > > Yours sincerely > > Best > > Gerard > -- Simon Cross Snr Scientist & Product Manager Molecular Discovery Ltd Tel 07980 572278 www.moldiscovery.com From owner-chemistry@ccl.net Tue Nov 24 12:55:00 2009 From: "odio(_)imre.oc.uh.cu" To: CCL Subject: CCL: dimensionless reaction coordinate Message-Id: <-40780-091124124520-13799-mbsDk/pSSeJCx7PyT6urxA]![server.ccl.net> X-Original-From: odio],[imre.oc.uh.cu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 24 Nov 2009 11:55:57 -0500 (CST) MIME-Version: 1.0 Sent to CCL by: odio(~)imre.oc.uh.cu Dear T. Manz: Thanks for sharing the program. I think is a nice solution for many problems and controversies. While trying to prove it in a simple case, I got the following error in the Matlab window: >> calculate p = 4 m = 2 nimages = 3 ??? Undefined function or variable 'textscan'. Error in ==> D:\transition_state_lateness_matlab_script_10_07_2009\calculate.m On line 27 ==> data = textscan(fid1,'%f %f %f', n_atoms); How could I overcome this? Thanks again, Oscar Odio > > Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com] > An early transition state resembles the reactants more than the products, > while a late transition state resembles the products more than the > reactants. Several postulates in chemistry and catalysis require a > quantitative measure of transition state lateness for their application. > These include the Hammond-Leffler postulate, the structure sensitivity > postulate, and the reactant sensitivity postulate. The Hammond-Leffler > postulate is taught in several college textbooks, and Hammonds 1955 > article describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has received > more than three thousand citations. However, until now there was no > universal method for quantifying transition state lateness from geometries > along a minimum energy reaction pathway. > > A new method published in the Journal of Computational Chemistry describes > a dimensionless reaction coordinate, W, that can be used to quantify the > relative lateness of transition states. W varies monotonically from 0 > (reactant) to 1 (product) along a minimum energy reaction pathway. Let WTS > denote the dimensionless reaction coordinate of the transition state. When > WTS < 0.5, the transition state is early. When WTS > 0.5, the transition > state is late. When WTS = 0.5, the transition state is equidistant between > reactants and products. This descriptor can be computed using only a > series of optimized geometries (aka images) along the minimum energy > reaction pathway. A minimum of three images (reactant, transition state, > and product) is required, and there is no maximum in the number of images > that can be used. > > Once optimized geometries along the minimum energy reaction pathway are > known, the time for computing W is a small fraction of a second. (The > equations for computing W of each image are simple algebraic equations.) > > A free program implementing the method is available at > > http://sourceforge.net/projects/drcs/ > > This type of analysis should be useful to those performing nudged elastic > band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction > coordinate (IRC) calculations. The method is applicable to both periodic > and nonperiodic systems and can be used for reactions occuring in the > gas-phase, in liquid-phase, in solids, or on surfaces. > > Link to the published abstract: > > http://www3.interscience.wiley.com/journal/122682417/abstract > > The article describes both the quantification of transition state lateness > and its application to several postulates in chemistry and catalysis. > > Tom Manz > > thomasamanz [at] gmail.com> > > From owner-chemistry@ccl.net Tue Nov 24 13:30:01 2009 From: "Carlos F. Lagos carlos^-^cbuc.cl" To: CCL Subject: CCL: Metabolite-structure prediction software requested Message-Id: <-40781-091124131406-7033-NOFQBK0Aivs/ku4b4wfBPA[]server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Type: multipart/alternative; boundary="----=_NextPart_000_002D_01CA6D17.A815B230" Date: Tue, 24 Nov 2009 15:06:07 -0300 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos.(!).cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_002D_01CA6D17.A815B230 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Gerard, if you know the chemical reactions involved in the metabolite generation, yuo can encode the and filter your database using Reactor from ChemAxon, free for academics QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 8330025 Santiago-Chile Phone: +56 2 3541911 I http://www.cbuc.cl _____ De: owner-chemistry+carlos==cbuc.cl(!)ccl.net [mailto:owner-chemistry+carlos==cbuc.cl(!)ccl.net] En nombre de Gerard Pujadas gerard.pujadas:_:gmail.com Enviado el: Martes, 24 de Noviembre de 2009 09:05 Para: Lagos, Carlos F Asunto: CCL: Metabolite-structure prediction software requested Dear CCL list members, I would like to transform a database of drugs (for instance, in SDF format) with good ADMET properties into another database (for instance, in SDF format too) that contains the predicted structures of the most probable human metabolites of the molecules in the input file. Is there such a software? Any help will be appreciated With many thanks in advances for your help Yours sincerely Best Gerard ------=_NextPart_000_002D_01CA6D17.A815B230 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Gerard, if = you know the chemical reactions involved in the metabolite generation, yuo can = encode the and filter your database using Reactor from ChemAxon, free for = academics

 =

QF = Carlos F. Lagos
Centre for Bioinformatics CBUC, Faculty of Biological = Sciences

Medicinal = Chemistry Laboratory MCL, Faculty of Chemistry
P. Universidad Catolica de Chile
Portugal 49, Zocalo I 8330025 Santiago-Chile
Phone: +56 2 3541911 I http://www.cbuc.cl

 

=

 

De: owner-chemistry+carlos=3D=3Dcbuc.cl(!)ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl(!)ccl.net] En nombre de Gerard Pujadas = gerard.pujadas:_:gmail.com
Enviado el: Martes, 24 de Noviembre de 2009 09:05
Para: Lagos, Carlos F =
Asunto: CCL: = Metabolite-structure prediction software requested

 

Dear CCL list = members,

I would like to transform a database of drugs (for instance, in SDF = format) with good ADMET properties into another database (for instance, in SDF = format too) that contains the predicted structures of the most probable human metabolites of the molecules in the input file.

Is there such a software?

Any help will be appreciated

With many thanks in advances for your help

Yours sincerely

Best

Gerard



__________ Information from ESET NOD32 Antivirus, version of = virus signature database 4633 (20091124) __________

The message = was checked by ESET NOD32 Antivirus.

http://www.eset.com
------=_NextPart_000_002D_01CA6D17.A815B230-- From owner-chemistry@ccl.net Tue Nov 24 14:04:01 2009 From: "=?ISO-8859-1?Q?Miquel_Sol=E0?= miquel.sola*udg.edu" To: CCL Subject: CCL: Quantifying the Hammond postulate Message-Id: <-40782-091124125015-14252-WLKTcWMloimdmWILcHdCGA]-[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Miquel_Sol=E0?= Content-Type: multipart/alternative; boundary="------------090801050300000903090307" Date: Tue, 24 Nov 2009 18:05:38 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Miquel_Sol=E0?= [miquel.sola*|*udg.edu] This is a multi-part message in MIME format. --------------090801050300000903090307 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Thomas, There is at least another universal method to quantify the transition state earliness or lateness based on quantum molecular similarity measures. Some references are: 1) J. Cioslowski, /Quantifying the Hammond postulate: intramolecular proton transfer in substituted hydrogen catecholate anions. /*/J/. Am. Chem. Soc. 116 (1994) 6756-6760.* 2) M. Solà, J. Mestres, R. Carbó and M. Duran. /Use of ab initio Quantum Molecular Similarities as an interpretative tool for the study of chemical reactions./ *J. Am. Chem. Soc. 116 (1994) 5909-5915.* 3) M. Solà and A. Toro-Labbé. /The Hammond postulate and the Principle of Maximum Hardness in Some Intramolecular Rearrangement Reactions./ *J. Phys. Chem. A, 103 (1999) 8847-8852.* Best regards, Miquel Solà Thomas A. Manz thomasamanz(a)gmail.com escribió: > Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com] > An early transition state resembles the reactants more than the products, while a late transition state resembles the products more than the reactants. Several postulates in chemistry and catalysis require a quantitative measure of transition state lateness for their application. These include the Hammond-Leffler postulate, the structure sensitivity postulate, and the reactant sensitivity postulate. The Hammond-Leffler postulate is taught in several college textbooks, and Hammonds 1955 article describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has received more than three thousand citations. However, until now there was no universal method for quantifying transition state lateness from geometries along a minimum energy reaction pathway. > > A new method published in the Journal of Computational Chemistry describes a dimensionless reaction coordinate, W, that can be used to quantify the relative lateness of transition states. W varies monotonically from 0 (reactant) to 1 (product) along a minimum energy reaction pathway. Let WTS denote the dimensionless reaction coordinate of the transition state. When WTS < 0.5, the transition state is early. When WTS > 0.5, the transition state is late. When WTS = 0.5, the transition state is equidistant between reactants and products. This descriptor can be computed using only a series of optimized geometries (aka images) along the minimum energy reaction pathway. A minimum of three images (reactant, transition state, and product) is required, and there is no maximum in the number of images that can be used. > > Once optimized geometries along the minimum energy reaction pathway are known, the time for computing W is a small fraction of a second. (The equations for computing W of each image are simple algebraic equations.) > > A free program implementing the method is available at > > http://sourceforge.net/projects/drcs/ > > This type of analysis should be useful to those performing nudged elastic band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction coordinate (IRC) calculations. The method is applicable to both periodic and nonperiodic systems and can be used for reactions occuring in the gas-phase, in liquid-phase, in solids, or on surfaces. > > Link to the published abstract: > > http://www3.interscience.wiley.com/journal/122682417/abstract > > The article describes both the quantification of transition state lateness and its application to several postulates in chemistry and catalysis. > > Tom Manz > > thomasamanz [at] gmail.com> > > > -- -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Miquel Solà Institut de Química Computacional i Departament de Química Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola(a)udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- --------------090801050300000903090307 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Dear Thomas,

There is at least another universal method to quantify the transition state earliness or lateness based on quantum molecular similarity measures. Some references are:

1) J. Cioslowski, Quantifying the Hammond postulate: intramolecular proton transfer in substituted hydrogen catecholate anions.
J. Am. Chem. Soc. 116 (1994) 6756-6760.
2) M. Solà, J. Mestres, R. Carbó and M. Duran. Use of ab initio Quantum Molecular Similarities as an interpretative tool for the study of chemical reactions. J. Am. Chem. Soc. 116 (1994) 5909-5915.
3) M. Solà and A. Toro-Labbé. The Hammond postulate and the Principle of Maximum Hardness in Some Intramolecular Rearrangement Reactions. J. Phys. Chem. A, 103 (1999) 8847-8852.

Best regards,

Miquel Solà


Thomas A. Manz thomasamanz(a)gmail.com escribió: 
Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com]
An early transition state resembles the reactants more than the products, while a late transition state resembles the products more than the reactants. Several postulates in chemistry and catalysis require a quantitative measure of transition state lateness for their application. These include the Hammond-Leffler postulate, the structure sensitivity postulate, and the reactant sensitivity postulate. The Hammond-Leffler postulate is taught in several college textbooks, and Hammonds 1955 article describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has received more than three thousand citations. However, until now there was no universal method for quantifying transition state lateness from geometries along a minimum energy reaction pathway.

A new method published in the Journal of Computational Chemistry describes a dimensionless reaction coordinate, W, that can be used to quantify the relative lateness of transition states. W varies monotonically from 0 (reactant) to 1 (product) along a minimum energy reaction pathway. Let WTS denote the dimensionless reaction coordinate of the transition state. When WTS < 0.5, the transition state is early. When WTS > 0.5, the transition state is late. When WTS = 0.5, the transition state is equidistant between reactants and products. This descriptor can be computed using only a series of optimized geometries (aka images) along the minimum energy reaction pathway. A minimum of three images (reactant, transition state, and product) is required, and there is no maximum in the number of images that can be used. 

Once optimized geometries along the minimum energy reaction pathway are known, the time for computing W is a small fraction of a second. (The equations for computing W of each image are simple algebraic equations.) 

A free program implementing the method is available at
 
http://sourceforge.net/projects/drcs/

This type of analysis should be useful to those performing nudged elastic band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction coordinate (IRC) calculations. The method is applicable to both periodic and nonperiodic systems and can be used for reactions occuring in the gas-phase, in liquid-phase, in solids, or on surfaces. 

Link to the published abstract:

http://www3.interscience.wiley.com/journal/122682417/abstract

The article describes both the quantification of transition state lateness and its application to several postulates in chemistry and catalysis. 

Tom Manz

thomasamanz [at] gmail.comE-mail to subscribers: CHEMISTRY(a)ccl.net or use:
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-- 

 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
 Miquel Solà                           
 Institut de Química Computacional i Departament de Química        
 Universitat de Girona                   
 Campus Montilivi
 17071 Girona, CATALONIA (Spain)          
 Phone +34.972.41.89.12
 Cellular-Phone:  +34.626.163.580
 FAX   +34.972.41.83.56                               
 World Wide Web: http://iqc.udg.es/~miquel/mike.html   
 e-mail: miquel.sola(a)udg.es                         
 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
--------------090801050300000903090307-- From owner-chemistry@ccl.net Tue Nov 24 15:44:01 2009 From: "Ivan Ufimtsev i.ufimtsev^^^gmail.com" To: CCL Subject: CCL: Announce: TeraChem, GPU-accelerated software for quantum chemistry Message-Id: <-40783-091124143718-5087-IPKz9kIaiddbn18+b0+KIA*o*server.ccl.net> X-Original-From: "Ivan Ufimtsev" Date: Tue, 24 Nov 2009 14:37:14 -0500 Sent to CCL by: "Ivan Ufimtsev" [i.ufimtsev]*[gmail.com] Dear CCL community, We're happy to announce that we have launched beta testing phase of TeraChem, general purpose quantum chemistry software designed to run on NVIDIA GPU architectures under a 64-bit Linux operating system. Some of TeraChem features include: *Restricted Hartree-Fock and Kohn-Sham single point energy and gradient calculations *Various DFT functionals (BLYP, B3LYP, PBE, etc) and DFT grids (800-80,000 grid points per atom) *Geometry optimization *Ab initio molecular dynamics (NVE and NVT ensembles) *Support of multiple-GPU systems To qualify, you must have a machine with 64-bit Linux installed and a CUDA 1.3-capable NVIDIA graphics card such as http://www.nvidia.com/object/product_geforce_gtx_280_us.html You can sign up for the beta testing at http://petachem.com/products.html A short user guide is available at http://petachem.com/doc/userguide.pdf Best, Ivan Ufimtsev i.ufimtsev-#-gmail.com From owner-chemistry@ccl.net Tue Nov 24 18:06:00 2009 From: "Thomas Manz thomasamanz() gmail.com" To: CCL Subject: CCL: Quantifying the Hammond postulate Message-Id: <-40784-091124165502-25524-2UvDrg0i7aOu/RjGoAbwNw-x-server.ccl.net> X-Original-From: Thomas Manz Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Nov 2009 16:22:52 -0500 MIME-Version: 1.0 Sent to CCL by: Thomas Manz [thomasamanz-$-gmail.com] Dear Miquel, I am familiar with the series of paper you mentioned. (The year on the first paper should be 1991.) If I understand correctly, all of the examples in those papers are unimolecular reactions. It's not clear to me how that approach could be conveniently applied to other types of systems. Sincerely, Tom 2009/11/24 Miquel Sol=E0 miquel.sola*udg.edu : > > Dear Thomas, > > There is at least another universal method to quantify the transition sta= te > earliness or lateness based on quantum molecular similarity measures. Som= e > references are: > > 1) J. Cioslowski, Quantifying the Hammond postulate: intramolecular proto= n > transfer in substituted hydrogen catecholate anions. > J. Am. Chem. Soc. 116 (1994) 6756-6760. > 2) M. Sol=E0, J. Mestres, R. Carb=F3 and M. Duran. Use of ab initio Quant= um > Molecular Similarities as an interpretative tool for the study of chemica= l > reactions. J. Am. Chem. Soc. 116 (1994) 5909-5915. > 3) M. Sol=E0 and A. Toro-Labb=E9. The Hammond postulate and the Principle= of > Maximum Hardness in Some Intramolecular Rearrangement Reactions. J. Phys. > Chem. A, 103 (1999) 8847-8852. > > Best regards, > > Miquel Sol=E0 > > > Thomas A. Manz thomasamanz(a)gmail.com escribi=F3: > > Sent to CCL by: "Thomas A. Manz" [thomasamanz*gmail.com] > An early transition state resembles the reactants more than the products, > while a late transition state resembles the products more than the > reactants. Several postulates in chemistry and catalysis require a > quantitative measure of transition state lateness for their application. > These include the Hammond-Leffler postulate, the structure sensitivity > postulate, and the reactant sensitivity postulate. The Hammond-Leffler > postulate is taught in several college textbooks, and Hammonds 1955 artic= le > describing it (J. Am. Chem.Soc. 77 (1955) 334-338.) has received more tha= n > three thousand citations. However, until now there was no universal metho= d > for quantifying transition state lateness from geometries along a minimum > energy reaction pathway. > A new method published in the Journal of Computational Chemistry describe= s a > dimensionless reaction coordinate, W, that can be used to quantify the > relative lateness of transition states. W varies monotonically from 0 > (reactant) to 1 (product) along a minimum energy reaction pathway. Let WT= S > denote the dimensionless reaction coordinate of the transition state. Whe= n > WTS < 0.5, the transition state is early. When WTS > 0.5, the transition > state is late. When WTS =3D 0.5, the transition state is equidistant betw= een > reactants and products. This descriptor can be computed using only a seri= es > of optimized geometries (aka images) along the minimum energy reaction > pathway. A minimum of three images (reactant, transition state, and produ= ct) > is required, and there is no maximum in the number of images that can be > used. > Once optimized geometries along the minimum energy reaction pathway are > known, the time for computing W is a small fraction of a second. (The > equations for computing W of each image are simple algebraic equations.) > A free program implementing the method is available at > > http://sourceforge.net/projects/drcs/ > This type of analysis should be useful to those performing nudged elastic > band (NEB), quadratic synrchronous transit (QST), or intrinsic reaction > coordinate (IRC) calculations. The method is applicable to both periodic = and > nonperiodic systems and can be used for reactions occuring in the gas-pha= se, > in liquid-phase, in solids, or on surfaces. > Link to the published abstract: > http://www3.interscience.wiley.com/journal/122682417/abstract > The article describes both the quantification of transition state latenes= s > and its application to several postulates in chemistry and catalysis. > Tom Manz > thomasamanz [at] gmail.comE-mail to subscribers: CHEMISTRY**ccl.net or us= e:> E-mail to administrators: CHEMISTRY-REQUEST**ccl.net or usehttp://www.ccl.net/chemist= ry/sub_unsub.shtml> Search Messages: > http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spam= mers.txt> > > -- > > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - > Miquel Sol=E0 > Institut de Qu=EDmica Computacional i Departament de Qu=EDmica > Universitat de Girona > Campus Montilivi > 17071 Girona, CATALONIA (Spain) > Phone +34.972.41.89.12 > Cellular-Phone: +34.626.163.580 > FAX +34.972.41.83.56 > World Wide Web: http://iqc.udg.es/~miquel/mike.html > e-mail: miquel.sola**udg.es > -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*= - > From owner-chemistry@ccl.net Tue Nov 24 18:41:01 2009 From: "Richard Harper drrwharper^gmail.com" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40785-091124120120-9923-qaeKozl9AY4FkotT/B5GBQ=-=server.ccl.net> X-Original-From: Richard Harper Content-Type: multipart/alternative; boundary=000e0cd3580afc92260479202ec1 Date: Tue, 24 Nov 2009 11:10:41 -0500 MIME-Version: 1.0 Sent to CCL by: Richard Harper [drrwharper]_[gmail.com] --000e0cd3580afc92260479202ec1 Content-Type: text/plain; charset=ISO-8859-1 Is anyone hosting the old QCPE files? Someone wanted one a few months ago, and it was unclear where to look. Dick ---------- Forwarded message ---------- > From: Yvonne Martin yvonnecmartin_._gmail.com Date: Sat, Nov 21, 2009 at 10:54 AM Subject: CCL: PLS implementation? To: "Harper, Richard W. " Joe, Try the SAMPLS program from QCPE. Yvonne Martin On Wed, Nov 18, 2009 at 6:01 PM, Joe Leonard jleonard42-$-gmail.com < owner-chemistry-#-ccl.net> wrote: > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, I would appreciate any pointers to PLS implementations that can > handle much larger number of X variables as compared to Y (to-be-fit) > variables. I recall that PLS was used in 3D QSAR applications because of > its stability in such cases, but it seems that individual implementations > differ in how this statement applies to them... > > 3D QSAR test sets w/ aligned compounds would also be of use - if people are > aware of such collections on-line. But the PLS engine(s) are my primary > search right now... > > Thanks in advance! > > Joe Leonard > jleonard42]=[gmail.com > -- > I have fought a good fight, > I have finished my course, > I have kept the faith. > EFL/11-6-09> E-mail to subscribers: CHEMISTRY-#-ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --000e0cd3580afc92260479202ec1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Is anyone hosting the old QCPE files?=A0 Someone wanted one a few months ag= o, and it was unclear where to look.

Dick

---------- Forwarded message ----------
From: Yvonne Martin yvonnecmartin_._gmai= l.com <owner-chemistry*ccl.net>
Date: Sat, Nov 21, 2009 at 10:54 AM
Subject: CCL: PLS implementation?To: "Harper, Richard W. " <drrwharper*gmail.com>


Joe,


Try = the SAMPLS program from QCPE.

Yvonne Martin

On Wed, Nov 18, 2009 at= 6:01 PM, Joe Leonard jleonard42-$-gmail.com <owner-chemistry-#-ccl.net> wro= te:

Sent to CCL by: Joe Leonard [jleonard42|gmail.com]
Folks, I would appreciate any pointers to PLS implementations that can hand= le much larger number of X variables as compared to Y (to-be-fit) variables= . =A0I recall that PLS was used in 3D QSAR applications because of its stab= ility in such cases, but it seems that individual implementations differ in= how this statement applies to them...

3D QSAR test sets w/ aligned compounds would also be of use - if people are= aware of such collections on-line. =A0But the PLS engine(s) are my primary= search right now...

Thanks in advance!

Joe Leonard
jleonard42]=3D[gmail.com=
--
I have fought a good fight,
I have finished my course,
I have kept the faith.
EFL/11-6-09




-=3D This is automatically added to each message by the mailing script =3D-
E-mail to subscribers: CHEMISTRY-#-ccl.net or use:
=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=

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--000e0cd3580afc92260479202ec1-- From owner-chemistry@ccl.net Tue Nov 24 20:46:01 2009 From: "Andrew Orry andy .. molsoft.com" To: CCL Subject: CCL: Free Webinars: MolSoft's New Desktop Chemistry Products Message-Id: <-40786-091124204212-15523-UI6tqm9BNCzcdESD3ZqyzQ .. server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Nov 2009 17:36:15 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy/a\molsoft.com] Please join us at one of our webinars to learn more about MolSoft's two new desktop chemistry products - ICM-Chemist and ICM-Chemist-Pro. Registration is free and more details can be found here: http://www.molsoft.com/training.html Registration also includes a 2 week full-feature trial version of the software so you can try out what you see in the webinar. ICM-Chemist has a full suite of programs for chemical drawing/editing, combinatorial library generation, chemical/pharmacophore searching, clustering, and enumeration. You can see the full feature list at http://www.molsoft.com/icm-chemist.html ICM-Chemist-Pro has a wide range of 3D chemistry tools including a 3D interactive ligand editor (including docking), chemical superposition and QSAR tools. You can see the full feature list at http://www.molsoft.com/icm-chemist-pro.html All MolSoft's software runs on Mac, Windows and Linux and we offer competitive pricing and licensing terms. The webinars are being offered at 9AM PST on the following dates: Tuesday December 1st for ICM-Chemist http://www.molsoft.com/icm-chemist-webinar.html Tuesday December 8th for ICM-Chemist-Pro http://www.molsoft.com/icm-chemist-pro-webinar.html Any questions please E-Mail andy=-=molsoft.com or call (858) 625 2000 x108. Thanks, Andrew Orry Senior Scientist, MolSoft LLC From owner-chemistry@ccl.net Tue Nov 24 21:20:01 2009 From: "Stephen Bowlus chezbowlus+*+comcast.net" To: CCL Subject: CCL: PLS implementation? Message-Id: <-40787-091124202916-30615-FgBBO3pa2QpcLDeJyx47FA*|*server.ccl.net> X-Original-From: Stephen Bowlus Content-Type: multipart/alternative; boundary=Apple-Mail-5--516988083 Date: Tue, 24 Nov 2009 16:56:09 -0800 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Stephen Bowlus [chezbowlus---comcast.net] --Apple-Mail-5--516988083 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit I was able to rescue a program earlier this year, at which time the collection was being curated by a (semi?) retired faculty member, whose name escapes me. Jan corresponded with this person, so he might come up with a name (since the archive search is currently disabled). Failing that, my original search for a curator was addressed to the chemistry department at IU; and they very helpfully forwarded my request. Good luck, Steve Bowlus On Nov 24, 2009, at 8:10 AM, Richard Harper drrwharper^gmail.com wrote: > Is anyone hosting the old QCPE files? Someone wanted one a few > months ago, and it was unclear where to look. > > Dick > > ---------- Forwarded message ---------- > From: Yvonne Martin yvonnecmartin_._gmail.com chemistry^ccl.net> > Date: Sat, Nov 21, 2009 at 10:54 AM > Subject: CCL: PLS implementation? > To: "Harper, Richard W. " > > > Joe, > > > Try the SAMPLS program from QCPE. > > Yvonne Martin > > On Wed, Nov 18, 2009 at 6:01 PM, Joe Leonard jleonard42-$-gmail.com > wrote: > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, I would appreciate any pointers to PLS implementations that > can handle much larger number of X variables as compared to Y (to-be- > fit) variables. I recall that PLS was used in 3D QSAR applications > because of its stability in such cases, but it seems that individual > implementations differ in how this statement applies to them... > > 3D QSAR test sets w/ aligned compounds would also be of use - if > people are aware of such collections on-line. But the PLS engine(s) > are my primary search right now... > > Thanks in advance! > > Joe Leonard > jleonard42]=[gmail.com > -- > I have fought a good fight, > I have finished my course, > I have kept the faith. > EFL/11-6-09 > > > > > -= This is automatically added to each message by the mailing script > =- > E-mail to subscribers: CHEMISTRY-#-ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use> => > Job: http://www.ccl.net/jobs> > > > --Apple-Mail-5--516988083 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable I was able to rescue a program = earlier this year, at which time the collection was being curated = by a (semi?) retired faculty member, whose name escapes me.  Jan = corresponded with this person, so he might come up with a name (since = the archive search is currently disabled).  Failing that, my = original search for a curator was addressed to the chemistry department = at IU; and they very helpfully forwarded my = request.

Good luck,
Steve = Bowlus

On Nov 24, 2009, at 8:10 AM, Richard = Harper drrwharper^gmail.com wrote:

Is anyone = hosting the old QCPE files?  Someone wanted one a few months ago, = and it was unclear where to look.

Dick

---------- Forwarded message ----------
From: = Yvonne Martin yvonnecmartin_._gmail.com <owner-chemistry^ccl.net>
Date: Sat, Nov 21, 2009 at 10:54 AM
Subject: CCL: PLS = implementation?
To: "Harper, Richard W. " <drrwharper^gmail.com>

<= br>Joe,


Try the SAMPLS program from QCPE.

Yvonne = Martin

On Wed, Nov 18, 2009 at 6:01 = PM, Joe Leonard jleonard42-$-gmail.com <owner-chemistry-#-ccl.net> wrote:
=

= Sent to CCL by: Joe Leonard [jleonard42|gmail.com]
Folks, I would appreciate any = pointers to PLS implementations that can handle much larger number of X = variables as compared to Y (to-be-fit) variables.  I recall that = PLS was used in 3D QSAR applications because of its stability in such = cases, but it seems that individual implementations differ in how this = statement applies to them...

3D QSAR test sets w/ aligned = compounds would also be of use - if people are aware of such collections = on-line.  But the PLS engine(s) are my primary search right = now...

Thanks in advance!

Joe Leonard
= jleonard42]=3D[gmail.com
--
I have fought a good = fight,
I have finished my course,
I have kept the faith.
= EFL/11-6-09




-=3D This is automatically added to = each message by the mailing script =3D-
E-mail to subscribers: CHEMISTRY-#-ccl.net or use:
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=
E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use
  =   http://www.ccl.net/cgi-bin/ccl/send_ccl_message
= =3D

Before posting, check wait time at: = http://www.ccl.net

Job: http://www.ccl.net/jobsConferences: http://server.ccl.net/chemistry/announcements/conference= s/

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= --Apple-Mail-5--516988083--