From owner-chemistry@ccl.net Mon Nov 15 04:42:01 2010
From: "dgd-.-uni-muenster.de" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: MOPAC update: DFT accuracy; Ligand binding energies
Message-Id: <-43167-101115043150-8017-6WBRAxGtVDVbvQBq6r8HcA%x%server.ccl.net>
X-Original-From: <dgd(0)uni-muenster.de>
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Date: Mon, 15 Nov 2010 10:31:38 +0100 (CET)
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Sent to CCL by: [dgd-*-uni-muenster.de]
There is an improved third-generation correction out now (
http://pubs.acs.org/doi/abs/10.1021/ct100408b ), which will be available in
MOPAC in the not too distant future.
Best wishes, Martin


David Gallagher wrote:
> MOPAC2009 update, October 2010

> Accuracy has been enhanced using correction terms for dispersion and
> H-bonding (PM6-DH2)

> • DFT accuracy
> "The performance of the improved correction is evaluated for PM6, AM1,
> OM3, and SCC-DFTB (enhanced by standard empirical dispersion
> corrections) with several test sets for noncovalent interactions and is
> shown to reach the quality of current DFT-D approaches for these types
> of problems." (1)

> • Ligand binding energies
> "This rescoring method is applied to a very challenging system, namely,
> the HIV-1 protease with a set of ligands. As opposed to the conventional
> DOCK procedure, the PM6-DH2 rescoring based on all of the terms
> distinguishes between binders and nonbinders and provides a reliable
> correlation of the theoretical and experimental binding free energies.
> Such a dramatic improvement, resulting from the PM6-DH2 rescoring of all
> the complexes, provides a valuable yet inexpensive tool for rational
> drug discovery and de novo ligand design." (2)

> • PM6 includes all 83 elements up to Bismuth, and MOPAC2009 remains free
> to academics

> • For more information visit:
> <http://cacheresearch.com/mopac.html>http://cacheresearch.com/mopac.html


> (1) A Transferable H-Bonding Correction for Semiempirical
> Quantum-Chemical Methods, Martin Korth, Michal Pitonak, Jan Rezac, and
> Pavel Hobza, J. Chem. Theory Comput. 2010, 6, 344–352

> (2) A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum
> Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding:
> HIV-1 Protease with 22 Ligands, Jindich Fanfrlk, Agnieszka K. Bronowska,
> Jan Rezac, Ondej Penosil, Jan Konvalinka, and Pavel Hobza, J. Phys.
> Chem. B, 2010, 114 (39), pp 12666–12678

-- 
Dr. Martin Korth
Max-Planck-Institut fur Kohlenforschung
E-mail: korth]|[mpi-muelheim.mpg.de


From owner-chemistry@ccl.net Mon Nov 15 05:16:00 2010
From: "David Livingstone davel[*]chemquestuk.com" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: Descriptors
Message-Id: <-43168-101114150900-20936-SD6n+YI/WZ0C5ccRzXd83A]-[server.ccl.net>
X-Original-From: "David Livingstone" <davel _ chemquestuk.com>
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Date: Sun, 14 Nov 2010 20:08:38 -0000
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Sent to CCL by: "David Livingstone" [davel,+,chemquestuk.com]
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Apologies for the tardy comment on this.

I wrote a review on descriptors for QSAR Modelling ("The Characterization =
of 
Chemical Structures Using Molecular Properties. A Survey" D.J. Livingstone=
, 
J. Chem. Inf. Comput. Sci., 40, 195-209, 2000) which I think is fairly 
accessible and also quite comprehensive. This was published 10 years ago 
so there will be some new ones missing but, quite frankly, not a great dea=
l 
has changed in that time. Roberto Todeschini wrote a much more complete 
handbook of molecular descriptors in 2000 as well which has now been 
updated ("Molecular Descriptors for chemoinformatics" 2 volumes!, R. 
Todeschini and V. Consonni, Wiley-VCH, 2009).

Some properties are important in their own right, of course, and I have 
reviewed these a bit more recently("Theoretical Property Predictions" D.J.=
 
Livingstone, Curr. Top. Med. Chem., 3, 1171-92, 2003).

Regards,

	Dave.



-- 
D.J. Livingstone                ChemQuest
                       Delamere House, 1 Royal Crescent,
                       Sandown. Isle of Wight UK PO36 8LZ 

Phone: +44 (0)1983 406832
e-mail davel]_[chemquestuk.com     www.chemquestuk.com
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<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt"><=
br />
</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">A=
pologies for the tardy comment on this.</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt"><=
br />
</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
">I wrote a review on descriptors for QSAR Modelling (&ldquo;The Character=
ization of 
Chemical Structures Using Molecular Properties. A Survey&rdquo; D.J. Livin=
gstone, 
<i>J. Chem. Inf. Comput. Sci</i>., <b>40</b>, 195-209, 2000) which I think=
 is fairly 
accessible and also quite comprehensive. This was published 10 years ago 
so there will be some new ones missing but, quite frankly, not a great dea=
l 
has changed in that time. Roberto Todeschini wrote a much more complete 
handbook of molecular descriptors in 2000 as well which has now been 
updated (&quot;Molecular Descriptors for chemoinformatics&quot; 2 volumes!=
, R. 
Todeschini and V. Consonni, Wiley-VCH, 2009).</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
"><br />
</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
">Some properties are important in their own right, of course, and I have 
reviewed these a bit more recently(&ldquo;Theoretical Property Predictions=
&rdquo; D.J. 
Livingstone, <i>Curr. Top. Med. Chem.</i>, <b>3</b>, 1171-92, 2003).</span=
></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
"><br />
</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
">Regards,</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
"><br />
</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
">&#160;&#160;&#160;&#160;&#160;&#160;&#160;Dave.</span></font></div>
<div align=3D"justify"><font face=3D"Arial"><span style=3D" font-size:12pt=
"><br />
</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt"><=
br />
</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt"><=
br />
</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">-=
- </span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">D=
.J. Livingstone&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160=
;&#160;&#160;&#160;&#160;&#160; ChemQuest</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">&=
#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#1=
60;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Delamere House, =
1 Royal Crescent,</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">&=
#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#1=
60;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; Sandown. Isle of=
 Wight UK PO36 8LZ </span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt"><=
br />
</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">P=
hone: +44 (0)1983 406832</span></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">e=
-mail davel]_[chemquestuk.com&#160;&#160;&#160;&#160; www.chemquestuk.com</s=
pan></font></div>
<div align=3D"left"><font face=3D"Arial"><span style=3D" font-size:12pt">-=
-----------------------------------------------------------------</span></=
font></div>
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From owner-chemistry@ccl.net Mon Nov 15 09:58:00 2010
From: "Andras Borosy andras.borosy^-^givaudan.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Descriptors
Message-Id: <-43169-101115094751-7000-SlGYGGzN40/oWCtOOtG77g^_^server.ccl.net>
X-Original-From: Andras Borosy <andras.borosy-*-givaudan.com>
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--=_alternative 00514181C12577DC_=--


From owner-chemistry@ccl.net Mon Nov 15 16:52:00 2010
From: "Maurizio Bronzetti mauriziospacezero-ccl{:}yahoo.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: MobileReagents 2.0
Message-Id: <-43170-101115125222-29648-CFYjEL0H+ZSG561nOz3BRg-#-server.ccl.net>
X-Original-From: Maurizio Bronzetti <mauriziospacezero-ccl*_*yahoo.com>
Content-Type: multipart/alternative; boundary="0-1444143112-1289843532=:58241"
Date: Mon, 15 Nov 2010 09:52:12 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Maurizio Bronzetti [mauriziospacezero-ccl-#-yahoo.com]
--0-1444143112-1289843532=:58241
Content-Type: text/plain; charset=us-ascii

Mobile Reagents v. 2.0 iPhone and iPod Touch* app released!
>> 
>>
>>Mobile Reagents gives you access to ~680,000 reagents for organic synthesis and 
>>screening compounds available from 22 suppliers. It supports name, formula and 
>>substructure searching. In version 2.0, users have the options of using 
>>Molecular Material Informatics' editor - Mobile Molecular DataSheet or MMDS - to 
>>create or edit chemical structures. Another important feature implemented in 
>>version 2.0 is the highlighting of query structures.
>> 
>>
>>In addition to drawing structure, thanks to the integration with the Optical 
>>Structure Recognition Application (OSRA), Mobile Reagent allows users to convert 
>>a snapshot of a structure taken with an iPhone or iPod Touch camera, into a mol, 
>>a smi file or into a "live" structure that can be used to search the database.
>> 
>>
>>Visit  Mobile Reagents at www.mobilereagents.com to learn 'MORE'.
>> 
>>
>>The MORE Team
>> 
>>
>>*internet connectivity required
--0-1444143112-1289843532=:58241
Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:verdana, helvetica, sans-serif;font-size:10pt"><div></div><div><font class="Apple-style-span" color="#5B5B5B" face="tahoma, 'new york', times, serif"><span class="Apple-style-span" style="font-size: small;"><i><font class="Apple-style-span" color="#000000" face="verdana, helvetica, sans-serif"><span class="Apple-style-span" style="font-style: normal;"><span class="Apple-style-span" style="font-family: 'times new roman', 'new york', times, serif; font-size: 16px; "><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium; "><div><div style="margin-top: 0px; margin-right:
 0px; margin-bottom: 0px; margin-left: 0px; font-family: verdana, helvetica, sans-serif; font-size: 10pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: verdana, helvetica, sans-serif; font-size: 10pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: times, serif; font-size: 12pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; font-size: medium; "><div style="margin-top: 0px; margin-right: 0px;
 margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: verdana, helvetica, sans-serif; font-size: 10pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0.0001pt; margin-left: 0px; line-height: normal; "><span style="font-family: Verdana, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">Mobile Reagents v. 2.0 iPhone and iPod Touch* app released!</span></span></p><div style="margin-bottom: 0.0001pt; line-height: normal; "><span style="font-family: Verdana, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">&nbsp;</span></span><span class="Apple-style-span" style="font-size: small;"><br class="webkit-block-placeholder"></span></div><p class="MsoNormal" style="margin-top: 0px;
 margin-right: 0px; margin-bottom: 0.0001pt; margin-left: 0px; line-height: normal; "><span style="font-family: Arial, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">Mobile Reagents gives you access to ~680,000 reagents for organic synthesis and screening compounds available from 22 suppliers. It supports&nbsp;name, formula and substructure searching. In version 2.0, users have the options of using Molecular Material Informatics' editor - Mobile Molecular DataSheet or MMDS - to create or edit chemical structures. Another important feature implemented in version 2.0 is the highlighting of query structures.</span></span></p><div style="margin-bottom: 0.0001pt; line-height: normal; "><span style="font-family: Arial, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">&nbsp;</span></span><span class="Apple-style-span" style="font-size: small;"><br
 class="webkit-block-placeholder"></span></div><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0.0001pt; margin-left: 0px; line-height: normal; "><span style="font-family: Arial, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">In addition to drawing structure, thanks to the integration with the Optical Structure Recognition Application (OSRA), Mobile Reagent allows users to convert a snapshot of a structure taken with an iPhone or iPod Touch camera, into a mol, a smi file or into a "live" structure that can be used to search the database.</span></span></p><div style="margin-bottom: 0.0001pt; line-height: normal; "><span style="font-family: Verdana, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">&nbsp;</span></span><span class="Apple-style-span" style="font-size: small;"><br class="webkit-block-placeholder"></span></div><p class="MsoNormal"
 style="margin-top: 0px; margin-right: 0px; margin-bottom: 0.0001pt; margin-left: 0px; line-height: normal; "><span style="font-family: Arial, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">Visit &nbsp;Mobile Reagents at&nbsp;</span><a rel="nofollow" target="_blank" href="http://www.mobilereagents.com/"><span style="color: blue; "><span class="Apple-style-span" style="font-size: small;">www.mobilereagents.com</span></span></a><span class="Apple-style-span" style="font-size: small;">&nbsp;to learn 'MORE'.</span></span><span class="Apple-style-span" style="font-size: small;"><span style="font-family: Verdana, sans-serif; color: black; "></span></span></p><div style="margin-bottom: 0.0001pt; line-height: normal; "><span style="font-family: Verdana, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">&nbsp;</span></span><br class="webkit-block-placeholder"></div><p class="MsoNormal"
 style="margin-top: 0px; margin-right: 0px; margin-bottom: 5pt; margin-left: 0px; line-height: normal; "><span style="font-family: Arial, sans-serif; color: black; "><span class="Apple-style-span" style="font-size: small;">The MORE Team</span></span><span class="Apple-style-span" style="font-size: small;"><span style="font-family: Verdana, sans-serif; color: black; "></span></span></p><div><span class="Apple-style-span" style="font-size: small;">&nbsp;</span><br class="webkit-block-placeholder"></div><p class="MsoNormal" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">*internet connectivity required</p></div></div></div></span></blockquote></div></div></div></div></div></div></span></blockquote></span></span></font></i></span></font></div><div style="font-family:verdana, helvetica, sans-serif;font-size:10pt"><div style="font-family:times new roman, new york, times, serif;font-size:12pt">


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