From owner-chemistry@ccl.net Mon Mar 11 07:34:01 2013 From: "Simon Cross simon^_^moldiscovery.com" To: CCL Subject: CCL: Anybody have pointers for protomer/tautomer ranking articles? Message-Id: <-48400-130311044957-31967-9pM+WR8BOeLJOLKh6eneBw * server.ccl.net> X-Original-From: Simon Cross Content-Type: multipart/alternative; boundary=14dae93404c9877c5b04d7a241ed Date: Mon, 11 Mar 2013 09:49:50 +0100 MIME-Version: 1.0 Sent to CCL by: Simon Cross [simon^-^moldiscovery.com] --14dae93404c9877c5b04d7a241ed Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hi Joe - we have a few papers in this area, the 2009 JCIM one is probably a good place to start: Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery Francesca Milletti and Anna Vulpetti *J. Chem. Inf. Model.*, *2010*, *50* (6), pp 1062=961074 Milletti F, Storchi L, Sforna G, Cruciani G. New and original pKa prediction method using grid molecular interaction fields. J Chem Inf Model. 2007 Nov-Dec;47(6):2172-81. Milletti F, Storchi L, Sforna G, Cross S, Cruciani G. Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J Chem Inf Model. 2009 Jan;49(1):68-75. Manchester J, Walkup G, Rivin O, You Z. Evaluation of pKa estimation methods on 211 druglike compounds. J Chem Inf Model. 2010 Apr 26;50(4):565-71. Milletti F, Storchi L, Cruciani G. Predicting protein pK(a) by environment similarity. Proteins. 2009 Aug 1;76(2):484-95. Cruciani G, Milletti F, Storchi L, Sforna G, Goracci L. In silico pKa prediction and ADME profiling. Chem Biodivers. 2009 Nov;6(11):1812-21. Cheers, Simon On Sun, Mar 10, 2013 at 2:54 PM, Joe Leonard jleonard42~~gmail.com < owner-chemistry|ccl.net> wrote: > Folks, I am interesting in learning of any preferably recent articles > discussing the state of the art of evaluating the likelihood of particula= r > protonization or tautomerization states of molecules. I will do a Google > Scholar search as well, but pinging CCL tends to be more rewarding, as I > sometimes find Google like "drinking from a firehose". In this case, I > hope that some of the authors of these articles peruse CCL... > > Thanks in advance! > > Joe Leonard > jleonard42\a/gmail.com > -- > "At least Loria gave something back to Canada with this trade." "Taking > from Montreal and giving back to Toronto is not really a recipe for peace > or goodwill." > > > > --14dae93404c9877c5b04d7a241ed Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Hi Joe - we have a few papers in this area, the 2009 JCIM = one is probably a good place to start:


Simon

<= div class=3D"gmail_extra">

On Sun, Mar 10= , 2013 at 2:54 PM, Joe Leonard jleonard42~~gma= il.com <owner-chemistry|ccl.net> wrote:
Folks, I= am interesting in learning of any preferably recent articles discussing th= e state of the art of evaluating the likelihood of particular protonization= or tautomerization states of molecules. =A0I will do a Google Scholar sear= ch as well, but pinging CCL tends to be more rewarding, as I sometimes find= Google like "drinking from a firehose". =A0In this case, I hope = that some of the authors of these articles peruse CCL...

Thanks in advance!

Joe Leonard
jleonar= d42\a/gmail.com
--
"At least Loria gave something back to=A0Canada with th= is trade." =A0"Taking from Montreal and giving back to=A0Toronto = is not really a recipe for peace or=A0goodwill."


=


--14dae93404c9877c5b04d7a241ed-- From owner-chemistry@ccl.net Mon Mar 11 13:56:01 2013 From: "=?ISO-8859-1?Q?Lu=EDs_Carlos_Filipe?= lcsfilipe%gmail.com" To: CCL Subject: CCL: Anybody have pointers for protomer/tautomer ranking articles? Message-Id: <-48401-130311130746-26345-M3wTSdQeb4nERTqA4i74Pg..server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Lu=EDs_Carlos_Filipe?= Content-Type: multipart/alternative; boundary=20cf3079b5eae4990104d7a9354a Date: Mon, 11 Mar 2013 18:07:40 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Lu=EDs_Carlos_Filipe?= [lcsfilipe-*-gmail.com] --20cf3079b5eae4990104d7a9354a Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Perhaps this might be of some use: Some Theoretical and Computational Aspects of the Inclusion of Proton Isomerism in the Protonation Equilibrium of Proteins https://pubs.acs.org/doi/abs/10.1021/jp002763e Best, Lu=EDs Filipe 2013/3/11 Simon Cross simon^_^moldiscovery.com > Hi Joe - we have a few papers in this area, the 2009 JCIM one is probably > a good place to start: > > Tautomer Preference in PDB Complexes and its Impact on Structure-Based > Drug Discovery > Francesca Milletti and Anna Vulpetti > *J. Chem. Inf. Model.*, *2010*, *50* (6), pp 1062=961074 > > Milletti F, Storchi L, Sforna G, Cruciani G. New and original pKa > prediction method using grid molecular interaction fields. J Chem Inf > Model. 2007 Nov-Dec;47(6):2172-81. > > Milletti F, Storchi L, Sforna G, Cross S, Cruciani G. Tautomer enumeratio= n > and stability prediction for virtual screening on large chemical database= s. > J Chem Inf Model. 2009 Jan;49(1):68-75. > > > Manchester J, Walkup G, Rivin O, You Z. Evaluation of pKa estimation > methods on 211 druglike compounds. J Chem Inf Model. 2010 Apr > 26;50(4):565-71. > > Milletti F, Storchi L, Cruciani G. Predicting protein pK(a) by environmen= t > similarity. Proteins. 2009 Aug 1;76(2):484-95. > > Cruciani G, Milletti F, Storchi L, Sforna G, Goracci L. In silico pKa > prediction and ADME profiling. Chem Biodivers. 2009 Nov;6(11):1812-21. > > Cheers, > > Simon > > > > On Sun, Mar 10, 2013 at 2:54 PM, Joe Leonard jleonard42~~gmail.com < > owner-chemistry%x%ccl.net > wrote: > >> Folks, I am interesting in learning of any preferably recent articles >> discussing the state of the art of evaluating the likelihood of particul= ar >> protonization or tautomerization states of molecules. I will do a Googl= e >> Scholar search as well, but pinging CCL tends to be more rewarding, as I >> sometimes find Google like "drinking from a firehose". In this case, I >> hope that some of the authors of these articles peruse CCL... >> >> Thanks in advance! >> >> Joe Leonard >> jleonard42\a/gmail.com >> -- >> "At least Loria gave something back to Canada with this trade." "Taking >> from Montreal and giving back to Toronto is not really a recipe for peac= e >> or goodwill." >> >> >> >> > --20cf3079b5eae4990104d7a9354a Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Perhaps this might be of some use:

Some Theoretical and Computationa= l Aspects of the Inclusion of Proton Isomerism in the Protonation Equilibri= um of Proteins
https://pubs.acs.org/doi/abs/10.1021/jp002763e

Best,

Lu=EDs Filipe

2013/3/11 = Simon Cross simon^_^moldiscovery.com <owner-chemistry{=}ccl.net>
Hi Joe - we have a few pape= rs in this area, the 2009 JCIM one is probably a good place to start:

Tautomer Preference in PDB Complexes and its Impact on Structure-Based = Drug Discovery
Francesca Milletti and Anna Vulpetti
J. Chem. Inf. Model., 2010, 50 (6), pp 1062=961074=

Millet= ti F, Storchi L,=20 Sforna G, Cruciani G. New and original pKa prediction method using grid=20 molecular interaction fields. J Chem Inf Model. 2007=20 Nov-Dec;47(6):2172-81.

M= illetti F,=20 Storchi L, Sforna G, Cross S, Cruciani G. Tautomer enumeration and=20 stability prediction for virtual screening on large chemical databases. J Chem Inf Model. 2009 Jan;49(1):68-75.

Manche= ster J, Walkup G, Rivin O, You Z. Evaluation of pKa estimation methods on 211 druglike=20 compounds. J Chem Inf Model. 2010 Apr 26;50(4):565-71.

Mille= tti F, Storchi L, Cruciani G. Predicting protein pK(a) by environment simil= arity. Proteins. 2009 Aug 1;76(2):484-95.

Crucia= ni G, Milletti F, Storchi L, Sforna G, Goracci L. In silico pKa prediction and ADME=20 profiling. Chem Biodivers. 2009 Nov;6(11):1812-21.

Cheers,

Simon



On Sun, Mar 10, 2013 at 2:54 PM, Joe Leonard jleonard42~~gmail.com <owner-chemistry%x= %ccl.net> wrote:
Folks, I= am interesting in learning of any preferably recent articles discussing th= e state of the art of evaluating the likelihood of particular protonization= or tautomerization states of molecules. =A0I will do a Google Scholar sear= ch as well, but pinging CCL tends to be more rewarding, as I sometimes find= Google like "drinking from a firehose". =A0In this case, I hope = that some of the authors of these articles peruse CCL...

Thanks in advance!

Joe Leonard
jleonar= d42\a/gmail.com
--
"At least Loria gave something back to=A0Canada with th= is trade." =A0"Taking from Montreal and giving back to=A0Toronto = is not really a recipe for peace or=A0goodwill."


=



--20cf3079b5eae4990104d7a9354a-- From owner-chemistry@ccl.net Mon Mar 11 20:36:00 2013 From: "Giuseppe Mallia g.mallia~!~imperial.ac.uk" To: CCL Subject: CCL: MSSC2013 - Ab initio Modelling in Solid State Chemistry - WEBSITES Message-Id: <-48402-130311183336-4054-4Rv8/p1PN7vBl3MeU3w+/A~!~server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Mon, 11 Mar 2013 18:33:34 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia]=[imperial.ac.uk] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ WORKSHOP ANNOUNCEMENTS MSSC2013 - Ab initio Modelling in Solid State Chemistry ==> Turin Edition (Experienced Users): Featuring CRYSTAL13 and CRYSCOR13 Torino, Italy, September 1-5, 2013 http://www.crystal.unito.it/MSSC2013/ ==> London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL London (UK), September 16-20, 2013 www3.imperial.ac.uk/MSSC2013 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2013 - Ab initio Modelling in Solid State Chemistry Turin Edition (Experienced Users): Featuring CRYSTAL13 and CRYSCOR13 Torino, Italy, September 1-5, 2013 Director: R. Dovesi http://www.crystal.unito.it/MSSC2013/ Its aim is to illustrate the features of the CRYSTAL13 and CRYSCOR13 programs. The school is addressed to all CRYSTAL's users, senior researchers and scientists with a good background in solid state chemistry and physics, who can take advantage of the two codes for their applications *** Workshop in memory of Cesare Pisani *** Torino, Italy, September 6-7, 2013 http://www.theochem.unito.it/WSSQC-13 On September 6-7th, 2013, a two-day workshop in memory of Cesare Pisani will follow the MSSC2013 School. The workshop celebrates the life and accomplishments of Cesare Pisani, during his more than fourty-year academic career, and provides an occasion to remember his contributions to computational solid state chemistry and physics. The program features talks by several eminent scientists on the recent development of theoretical and computational chemistry of crystalline systems. Registration will be open soon. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2013 - Ab initio Modelling in Solid State Chemistry London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL London (UK), September 16-20, 2013 Directors: N.M. Harrison - G. Mallia www3.imperial.ac.uk/MSSC2013 The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL and CRYSCOR. Registration will be open soon. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~