From owner-chemistry@ccl.net Wed Oct  3 04:35:01 2012
From: "Prija Ponnan prija.ponnan[A]gmail.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Decoy Dataset for Bcr-Abl Kinase
Message-Id: <-47699-121003042829-850-dVnRW+CHROUXSqjyGFt9/w() server.ccl.net>
X-Original-From: Prija Ponnan <prija.ponnan{=}gmail.com>
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Date: Wed, 3 Oct 2012 13:57:41 +0530
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Sent to CCL by: Prija Ponnan [prija.ponnan|,|gmail.com]
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Hello

Can anyone help me out with commercial/non-commercial decoy datasets for
Bcr-Abl kinase.

Thank You

Prija Ponnan

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Hello<br><br>Can anyone help me out with commercial/non-commercial decoy da=
tasets for Bcr-Abl kinase.<br><br>Thank You<br><br clear=3D"all">Prija Ponn=
an=20
<div>=A0</div><br>

--047d7b339859e4aacc04cb236b61--


From owner-chemistry@ccl.net Wed Oct  3 07:04:01 2012
From: "Sergio Manzetti sergio.manzetti*_*gmx.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47700-121003060433-3977-dzJt3c2fwOsfLWm6SuBJdw-#-server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti:gmx.com>
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Date: Wed, 03 Oct 2012 12:04:16 +0200
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Sent to CCL by: "Sergio Manzetti" [sergio.manzetti|a|gmx.com]
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Dear CCLrs, how can one extract the parameters of "resonance energy" (Randic, 2003) from a SCF calculation of a neutral ring system?

 Thanks

 Sergio

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<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>Dear CCL=
rs, how can one extract the parameters of "resonance energy"&nbsp; (Randic,=
 2003) from a&nbsp; SCF calculation&nbsp; of a neutral ring system?<br />=
=20
<br />=20
Thanks<br />=20
<br />=20
Sergio</span></span>

--========GMXBoundary93601349258656871059--


From owner-chemistry@ccl.net Wed Oct  3 08:08:01 2012
From: "Jan H Jensen jhjensen ~ chem.ku.dk" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry Highlights: September issue
Message-Id: <-47701-121003033046-32262-6rjfma+RD+CcVDiUFt00Vg..server.ccl.net>
X-Original-From: "Jan H Jensen" <jhjensen*chem.ku.dk>
Date: Wed, 3 Oct 2012 03:30:45 -0400


Sent to CCL by: "Jan H Jensen" [jhjensen-x-chem.ku.dk]
The September issue of Computational Chemistry Highlights is out.
http://www.compchemhighlights.org/2012_09_01_archive.html

CCH is an overlay journal that identifies the most important papers in computational and theoretical 
chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free 
resource run by scientists for scientists.

Table of content for this issue features contributions from CCH editors Steven Bachrach, G. Andres 
Cisneros, and Jan Jensen:

Stable Alkanes Containing Very Long CarbonCarbon Bonds
http://www.compchemhighlights.org/2012/09/stable-alkanes-containing-very-long.html

A simple, exact DFT embedding exchange
http://www.compchemhighlights.org/2012/09/a-simple-exact-dft-embedding-exchange.html

Dynamics, transition states, and timing of bond formation in Diels-Alder reaktions
http://www.compchemhighlights.org/2012/09/dynamics-transition-states-and-timing.html

The Last Globally Stable Extended Alkane
http://www.compchemhighlights.org/2012/09/the-last-globally-stable-extended-alkane.html

Dispersion corrections and bio-molecular structure and reactivity
http://www.compchemhighlights.org/2012/09/dispersion-corrections-and-bio.html

Interested in more? There are many ways to subscribe to CCH updates.
http://www.compchemhighlights.org/p/get-cch-updates.html


From owner-chemistry@ccl.net Wed Oct  3 08:43:00 2012
From: "Marcin Sterniczuk m.sterniczuk_+_ichtj.waw.pl" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: Supramolecular Method (with BSSE) and Energy of Interaction
Message-Id: <-47702-121003054342-690-nRtE7rAGxnkKCb45fbJ4rg/a\server.ccl.net>
X-Original-From: "Marcin  Sterniczuk" <m.sterniczuk(0)ichtj.waw.pl>
Date: Wed, 3 Oct 2012 05:43:40 -0400


Sent to CCL by: "Marcin  Sterniczuk" [m.sterniczuk^^ichtj.waw.pl]
Hello,

I want calculate energy interaction beetwen 2 molecules with supramolecular methods (of course with BSSE correction). In Gaussian we define a spin and charge for our system and parts of system beetwen we want compute energy interaction. For example in NaCl we define 0 1 (0-charge 1-spin) for molecule NaCl, and next 1 2 for Na+ and -1 2 for Cl-. Then the program compute energy interaction beetwen this atoms (only culombic?). This energy is probably only culombic. Probably NaCl have also little part of energy from "covalent" interaction (in every bond we have not only ionic or covalent bond but a some mix of them). It is possible to use supramolecular method to compute balance beetween ion and covalent character of bond? If we define 0 for charge and 1 for spin for Na and also Cl atom when we compute NaCl bond energy then the interaction energy is different in output file. Of course we usually now which charge and spin give in our partial atoms or parts of bigger molecule, but not every time.


From owner-chemistry@ccl.net Wed Oct  3 10:41:00 2012
From: "Robert W. Gora robert.gora()pwr.wroc.pl" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47703-121003104018-16697-T6LRId/j8ATa682wA+PshA * server.ccl.net>
X-Original-From: "Robert W. Gora" <robert.gora!A!pwr.wroc.pl>
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Date: Wed, 03 Oct 2012 16:40:11 +0200 (CEST)
MIME-version: 1.0


Sent to CCL by: "Robert W. Gora" [robert.gora-#-pwr.wroc.pl]
  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

--Boundary_(ID_+Dxu7ZOncyfUCEMrUlrMHQ)
Content-type: TEXT/PLAIN; charset=ISO-8859-15; format=flowed
Content-transfer-encoding: 8BIT

> Dear CCLrs, how can one extract the parameters of "resonance energy"
> (Randic, 2003) from a SCF calculation of a neutral ring system?

One cannot, in my opinion you need a vb code for that :) Have a look at Rashid
et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t]
Try van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro.

Cheers,
Robert

--
Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info]
[http://www.researchgate.net/profile/Robert_Gora]
[http://www.researcherid.com/rid/B-3919-2010]

--Boundary_(ID_+Dxu7ZOncyfUCEMrUlrMHQ)--


From owner-chemistry@ccl.net Wed Oct  3 11:18:00 2012
From: "Sergio Manzetti sergio.manzetti^-^gmx.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47704-121003111103-29464-+PuBWMeW6n3BXZDYsiUzyw__server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti() gmx.com>
Content-Type: multipart/alternative;
 boundary="========GMXBoundary93581349277053427384"
Date: Wed, 03 Oct 2012 17:10:53 +0200
MIME-Version: 1.0


Sent to CCL by: "Sergio Manzetti" [sergio.manzetti{=}gmx.com]
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Difficult indeed Roberto!

 Is there a way of mapping the resonance energy or conjugation pattern straight from a SCF calculation?



----- Original Message -----
> From: Robert W. Gora robert.gora()pwr.wroc.pl
Sent: 10/03/12 04:40 PM
To: Manzetti, Sergio 
Subject: CCL: Resonance energy

 > Dear CCLrs, how can one extract the parameters of "resonance energy" > (Randic, 2003) from a SCF calculation of a neutral ring system? One cannot, in my opinion you need a vb code for that :) Have a look at Rashid et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t] Try van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro. Cheers, Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010]

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<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'>Difficul=
t indeed Roberto!<br />=20
<br />=20
Is there a way of mapping the resonance energy or conjugation pattern strai=
ght from a SCF calculation?<br />=20
<br />=20
<br />=20
<br />=20
<p style=3D"margin:0px; padding:0px;" >=20
	=C2=A0</p>=20
<blockquote style=3D"border-left: 1px solid #CCC; padding-left: 5px; margin=
-left: 5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" type=
=3D"cite">=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">----- =
Original Message -----</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">From: =
Robert W. Gora robert.gora()pwr.wroc.pl</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">Sent: =
10/03/12 04:40 PM</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">To: Ma=
nzetti, Sergio </span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">Subjec=
t: CCL: Resonance energy</span></span></p>=20
	<br />=20
	<div>=20
		<div>=20
			<pre style=3D"white-space: pre-wrap; word-wrap: break-word; font-size:11=
;pre">=20
&gt; Dear CCLrs, how can one extract the parameters of "resonance energy"=
=20
&gt; (Randic, 2003) from a SCF calculation of a neutral ring system?=20

One cannot, in my opinion you need a vb code for that :) Have a look at Ras=
hid=20
et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t]=20
Try van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro.=20

Cheers,=20
Robert=20

--=20
Robert W. G=C3=B3ra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.=
info]=20
[http://www.researchgate.net/profile/Robert_Gora]=20
[http://www.researcherid.com/rid/B-3919-2010]</pre>=20
		</div>=20
	</div>=20
</blockquote>=20
<p style=3D"margin:0px; padding:0px;" >=20
	=C2=A0</p>=20
<br />=20
</span></span>

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From owner-chemistry@ccl.net Wed Oct  3 12:37:00 2012
From: "Robert W. Gora robert.gora%%pwr.wroc.pl" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47705-121003123547-16531-tuBSF9fsUooJQWlnT6wr2w|server.ccl.net>
X-Original-From: "Robert W. Gora" <robert.gora[-]pwr.wroc.pl>
Content-type: multipart/mixed; boundary="Boundary_(ID_b8TUY8Yc2PrgYRHZtyyM2w)"
Date: Wed, 03 Oct 2012 18:35:40 +0200 (CEST)
MIME-version: 1.0


Sent to CCL by: "Robert W. Gora" [robert.gora-x-pwr.wroc.pl]
  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

--Boundary_(ID_b8TUY8Yc2PrgYRHZtyyM2w)
Content-type: TEXT/PLAIN; charset=utf-8; format=flowed
Content-transfer-encoding: 8BIT

> Difficult indeed Roberto!
>
> Is there a way of mapping the resonance energy or conjugation pattern
> straight from a SCF calculation?

:) Well nothing out of the box, but you could contact Yirong Mo who is using a
method called block localized wavefunction approach (BLW), but actually what
you can get is a mixture of delocalization and resonance contributions -
something close to Huckel's delocalization energy. You will find the
references in the Rashid's article I have sent you.

Best,
Roberto

> ----- Original Message -----
>> From: Robert W. Gora robert.gora()pwr.wroc.pl
> Sent: 10/03/12 04:40 PM To: Manzetti, Sergio Subject: CCL: Resonance energy
>
> > Dear CCLrs, how can one extract the parameters of "resonance energy" >
> > (Randic, 2003) from a SCF calculation of a neutral ring system? One
> > cannot, in my opinion you need a vb code for that :) Have a look at Rashid
> > et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t] Try
> > van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro. Cheers,
> > Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT
> > [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora]
> > [http://www.researcherid.com/rid/B-3919-2010]

--
Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info]
[http://www.researchgate.net/profile/Robert_Gora]
[http://www.researcherid.com/rid/B-3919-2010]

--Boundary_(ID_b8TUY8Yc2PrgYRHZtyyM2w)--


From owner-chemistry@ccl.net Wed Oct  3 14:00:00 2012
From: "Sergio Manzetti sergio.manzetti[-]gmx.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47706-121003134929-24294-/jgHoIzzWk9UoKMjo01e8g/./server.ccl.net>
X-Original-From: "Sergio Manzetti" <sergio.manzetti~~gmx.com>
Content-Type: multipart/alternative;
 boundary="========GMXBoundary93591349286558367240"
Date: Wed, 03 Oct 2012 19:49:18 +0200
MIME-Version: 1.0


Sent to CCL by: "Sergio Manzetti" [sergio.manzetti*|*gmx.com]
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Is this still a programming approach, or it a estimation from SCF data?

 (I am not a programmer)

 Cheers
----- Original Message -----
> From: Robert W. Gora robert.gora%%pwr.wroc.pl
Sent: 10/03/12 06:35 PM
To: Manzetti, Sergio 
Subject: CCL: Resonance energy

 > Difficult indeed Roberto! > > Is there a way of mapping the resonance energy or conjugation pattern > straight from a SCF calculation? :) Well nothing out of the box, but you could contact Yirong Mo who is using a method called block localized wavefunction approach (BLW), but actually what you can get is a mixture of delocalization and resonance contributions - something close to Huckel's delocalization energy. You will find the references in the Rashid's article I have sent you. Best, Roberto > ----- Original Message ----- >> From: Robert W. Gora robert.gora()pwr.wroc.pl > Sent: 10/03/12 04:40 PM To: Manzetti, Sergio Subject: CCL: Resonance energy > > > Dear CCLrs, how can one extract the parameters of "resonance energy" > > > (Randic, 2003) from a SCF calculation of a neutral ring system? One > > cannot, in my opinion you need a vb code for that :) Have a look at Rashid > > et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t] Try > > van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro. Cheers, > > Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT > > [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] > > [http://www.researcherid.com/rid/B-3919-2010] -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010]

--========GMXBoundary93591349286558367240
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Content-Transfer-Encoding: quoted-printable

<span style=3D'font-family:Verdana'><span style=3D'font-size:12px'><br />=
=20
Is this still a programming approach, or it a estimation from SCF data?<br =
/>=20
<br />=20
(I am not a programmer)<br />=20
<br />=20
Cheers<br />=20
<p style=3D"margin:0px; padding:0px;" >=20
	=C2=A0</p>=20
<blockquote style=3D"border-left: 1px solid #CCC; padding-left: 5px; margin=
-left: 5px; margin-bottom: 0px; margin-top: 0px; margin-right: 0px;" type=
=3D"cite">=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">----- =
Original Message -----</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">From: =
Robert W. Gora robert.gora%%pwr.wroc.pl</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">Sent: =
10/03/12 06:35 PM</span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">To: Ma=
nzetti, Sergio </span></span></p>=20
	<p style=3D"margin:0px; padding:0px;" >=20
		<span style=3D"font-family:Verdana"><span style=3D"font-size:12px">Subjec=
t: CCL: Resonance energy</span></span></p>=20
	<br />=20
	<div>=20
		<div>=20
			<pre style=3D"white-space: pre-wrap; word-wrap: break-word; font-size:11=
;pre">=20
&gt; Difficult indeed Roberto!=20
&gt;=20
&gt; Is there a way of mapping the resonance energy or conjugation pattern=
=20
&gt; straight from a SCF calculation?=20

:) Well nothing out of the box, but you could contact Yirong Mo who is usin=
g a=20
method called block localized wavefunction approach (BLW), but actually wha=
t=20
you can get is a mixture of delocalization and resonance contributions -=20
something close to Huckel's delocalization energy. You will find the=20
references in the Rashid's article I have sent you.=20

Best,=20
Roberto=20

&gt; ----- Original Message -----=20
&gt;&gt; From: Robert W. Gora robert.gora()pwr.wroc.pl=20
&gt; Sent: 10/03/12 04:40 PM To: Manzetti, Sergio Subject: CCL: Resonance e=
nergy=20
&gt;=20
&gt; &gt; Dear CCLrs, how can one extract the parameters of "resonance ener=
gy" &gt;=20
&gt; &gt; (Randic, 2003) from a SCF calculation of a neutral ring system? O=
ne=20
&gt; &gt; cannot, in my opinion you need a vb code for that :) Have a look =
at Rashid=20
&gt; &gt; et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp2111=
05t] Try=20
&gt; &gt; van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro.=
 Cheers,=20
&gt; &gt; Robert -- Robert W. G=C3=B3ra, Theoretical Chemistry Group, ICHFi=
T, WUT=20
&gt; &gt; [http://zcht.info] [http://www.researchgate.net/profile/Robert_Go=
ra]=20
&gt; &gt; [http://www.researcherid.com/rid/B-3919-2010]=20

--=20
Robert W. G=C3=B3ra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.=
info]=20
[http://www.researchgate.net/profile/Robert_Gora]=20
[http://www.researcherid.com/rid/B-3919-2010]</pre>=20
		</div>=20
	</div>=20
</blockquote>=20
<p style=3D"margin:0px; padding:0px;" >=20
	=C2=A0</p>=20
<br />=20
</span></span>

--========GMXBoundary93591349286558367240--


From owner-chemistry@ccl.net Wed Oct  3 17:33:01 2012
From: "Salter-Duke, Brian James - brian.james.duke*gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL:G: Resonance energy
Message-Id: <-47707-121003171656-14746-fBht3qFGN25AyEERTNH8gw__server.ccl.net>
X-Original-From: "Salter-Duke, Brian James -" <brian.james.duke],[gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=windows-1252
Date: Thu, 4 Oct 2012 07:16:45 +1000
MIME-Version: 1.0


Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke^^^gmail.com]
On Wed, Oct 03, 2012 at 04:40:11PM +0200, Robert W. Gora robert.gora()pwr.wroc.pl wrote:
> >Dear CCLrs, how can one extract the parameters of "resonance energy"
> >(Randic, 2003) from a SCF calculation of a neutral ring system?
> 
> One cannot, in my opinion you need a vb code for that :) Have a look at Rashid
> et al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t]
> Try van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro.

An excellent paper indeed. You can also try VB2000, which is now
released with GAMESS(US), and also has a stand-alone version. I am
working on a new way of getting VB2000 to work with Gaussian. VB2000 can
also calculate SCVB directly [See Karadakov et al J. Phys. Chem. A,
2012, 116 (26), pp 7238–7244], which uses both Cooper's Molpro code and
VB2000]. In fairness, as I am an author of VB2000, many people use the
XMVB code. I am not sure whether Gordon Gallup's CRUNCH program is
still available, That is pretty well all the VB programs.  See
http://en.wikipedia.org/wiki/Valence_bond_codes.

Cheers, Brian.

> Cheers,
> Robert
> 
> --
> Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info]
> [http://www.researchgate.net/profile/Robert_Gora]
> [http://www.researcherid.com/rid/B-3919-2010]


-- 
   Brian Salter-Duke (Brian Duke)   Brian.Salter-Duke,,monash.edu
                    Adjunct Associate Professor
            Monash Institute of Pharmaceutical Sciences
      Monash University Parkville Campus, VIC 3052, Australia


From owner-chemistry@ccl.net Wed Oct  3 19:03:00 2012
From: "=?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= adrian.cereto{}gmail.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Decoy Dataset for Bcr-Abl Kinase
Message-Id: <-47708-121003173308-15799-rVN79bl87oA1GRUx2nLK0A|*|server.ccl.net>
X-Original-From: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= <adrian.cereto++gmail.com>
Content-Type: multipart/alternative; boundary=14dae9340ec120082b04cb2e625a
Date: Wed, 3 Oct 2012 23:32:41 +0200
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Sent to CCL by: =?UTF-8?Q?Adri=C3=A0_Cereto_Massagu=C3=A9?= [adrian.cereto%a%gmail.com]
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Hello,

If you have a set of known active ligands (try
BindingDB<http://www.bindingdb.org>for that), you can create your own
set of decoys using
DecoyFinder <http://urvnutrigenomica-ctns.github.com/DecoyFinder/>.

I hope it helps,

Adri=C3=A0

2012/10/3 Prija Ponnan prija.ponnan[A]gmail.com <owner-chemistry.:.ccl.net>

> Hello
>
> Can anyone help me out with commercial/non-commercial decoy datasets for
> Bcr-Abl kinase.
>
> Thank You
>
> Prija Ponnan
>
>
>

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Hello,<br><br>If you have a set of known active ligands (try=C2=A0 <a href=
=3D"http://www.bindingdb.org">BindingDB</a> for that), you can create your =
own set of decoys using <a href=3D"http://urvnutrigenomica-ctns.github.com/=
DecoyFinder/">DecoyFinder</a>.<br>

<br>I hope it helps,<br><br>Adri=C3=A0<br><br><div class=3D"gmail_quote">20=
12/10/3 Prija Ponnan prija.ponnan[A]<a href=3D"http://gmail.com">gmail.com<=
/a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry.:.ccl.net" target=
=3D"_blank">owner-chemistry.:.ccl.net</a>&gt;</span><br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">Hello<br><br>Can anyone help me out with com=
mercial/non-commercial decoy datasets for Bcr-Abl kinase.<br><br>Thank You<=
span class=3D"HOEnZb"><font color=3D"#888888"><br>

<br clear=3D"all">Prija Ponnan=20
<div>=C2=A0</div><br>
</font></span></blockquote></div><br>

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From owner-chemistry@ccl.net Wed Oct  3 21:12:01 2012
From: "Amy Austin amy_jean_austin!^!yahoo.com" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: Resonance energy
Message-Id: <-47709-121003191054-20903-UGblJhHCRhLlm/aY0tUb9g+/-server.ccl.net>
X-Original-From: Amy Austin <amy_jean_austin]~[yahoo.com>
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Date: Wed, 3 Oct 2012 16:10:47 -0700 (PDT)
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Sent to CCL by: Amy Austin [amy_jean_austin.:.yahoo.com]
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Hi Sergio,=0A=0AMaybe my thinking is too simplistic. It seems like you coul=
d calculate the predicted value for the enthalpy of complete hydrogenation =
of your system which would be N times (N=3D# double bonds) that of one doub=
le bond). Then subtract the actual predicted value for the complete hydroge=
nation (which will be less due to the resonance stabilization). That differ=
ence should be the resonance energy of the system.=0A=0AOpinions to this te=
chnique are welcome - Please reply privately.=0A=0AI don't recommend using =
HF values for the resonance energy. I think you need to include instantaneo=
us correlation at some level in order to have meaningful results. If you ne=
ed to conserve on CPU time, I would recommend a DFT.=0A=0AHope this helps!=
=0A=0AAmy=0A=0A=0A=0A=0A________________________________=0A From: Sergio Ma=
nzetti sergio.manzetti^-^gmx.com <owner-chemistry..ccl.net>=0ATo: "Austin, A=
my J " <amy_jean_austin..yahoo.com> =0ASent: Wednesday, October 3, 2=
012 11:10 AM=0ASubject: CCL: Resonance energy=0A =0A=0ADifficult indeed Rob=
erto!=0A=0AIs there a way of mapping the resonance energy or conjugation pa=
ttern straight from a SCF calculation?=0A=0A=0A=0A=0A=A0=0A----- Original M=
essage -----=0A>From: Robert W. Gora robert.gora()pwr.wroc.pl=0A>Sent: 10/0=
3/12 04:40 PM=0A>To: Manzetti, Sergio =0A>Subject: CCL: Resonance energy=0A=
>=0A>> Dear CCLrs, how can one extract the parameters of "resonance energy"=
 =0A> (Randic, 2003) from a SCF calculation of a neutral ring system?  One =
cannot, in my opinion you need a vb code for that :) Have a look at Rashid =
=0Aet al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.1021/jp211105t] =
=0ATry van Lenthe's from gamess(uk) or Cooper's SCVB from Molcas/Molpro.  C=
heers, =0ARobert  -- =0ARobert W. G=F3ra, Theoretical Chemistry Group, ICHF=
iT, WUT [http://zcht.info] =0A[http://www.researchgate.net/profile/Robert_G=
ora] =0A[http://www.researcherid.com/rid/B-3919-2010]
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:12pt">Hi Sergio,<br><br>May=
be my thinking is too simplistic. It seems like you could calculate the pre=
dicted value for the enthalpy of complete hydrogenation of your system whic=
h would be N times (N=3D# double bonds) that of one double bond). Then subt=
ract the actual predicted value for the complete hydrogenation (which will =
be less due to the resonance stabilization). That difference should be the =
resonance energy of the system.<br><br>Opinions to this technique are welco=
me - Please reply privately.<br><br>I don't recommend using HF values for t=
he resonance energy. I think you need to include instantaneous correlation =
at some level in order to have meaningful results. If you need to conserve =
on CPU time, I would recommend a DFT.<br><br>Hope this helps!<br><br>Amy<br=
><div><span><br></span></div><div><br></div>  <div style=3D"font-family:
 times new roman, new york, times, serif; font-size: 12pt;"> <div style=3D"=
font-family: times new roman, new york, times, serif; font-size: 12pt;"> <d=
iv dir=3D"ltr"> <font face=3D"Arial" size=3D"2"> <hr size=3D"1">  <b><span =
style=3D"font-weight:bold;">From:</span></b> Sergio Manzetti sergio.manzett=
i^-^gmx.com &lt;owner-chemistry..ccl.net&gt;<br> <b><span style=3D"font-weig=
ht: bold;">To:</span></b> "Austin, Amy J " &lt;amy_jean_austin..yaho=
o.com&gt; <br> <b><span style=3D"font-weight: bold;">Sent:</span></b> Wedne=
sday, October 3, 2012 11:10 AM<br> <b><span style=3D"font-weight: bold;">Su=
bject:</span></b> CCL: Resonance energy<br> </font> </div> <br>=0A<meta htt=
p-equiv=3D"x-dns-prefetch-control" content=3D"off"><div id=3D"yiv1211835063=
"><span style=3D"font-family:Verdana;"><span style=3D"font-size:12px;">Diff=
icult indeed Roberto!<br> =0A<br> =0AIs there a way of mapping the resonanc=
e energy or conjugation pattern straight from a SCF calculation?<br> =0A<br=
> =0A<br> =0A<br> =0A<div style=3D"margin:0px;padding:0px;"> =0A=09&nbsp;</=
div> =0A<blockquote style=3D"border-left:1px solid #CCC;padding-left:5px;ma=
rgin-left:5px;margin-bottom:0px;margin-top:0px;margin-right:0px;" type=3D"c=
ite"> =0A=09<div style=3D"margin:0px;padding:0px;"> =0A=09=09<span style=3D=
"font-family:Verdana;"><span style=3D"font-size:12px;">----- Original Messa=
ge -----</span></span></div> =0A=09<div style=3D"margin:0px;padding:0px;"> =
=0A=09=09<span style=3D"font-family:Verdana;"><span style=3D"font-size:12px=
;">From: Robert W. Gora robert.gora()<a target=3D"_blank" href=3D"http://pw=
r.wroc.pl/">pwr.wroc.pl</a></span></span></div> =0A=09<div style=3D"margin:=
0px;padding:0px;"> =0A=09=09<span style=3D"font-family:Verdana;"><span styl=
e=3D"font-size:12px;">Sent: 10/03/12 04:40 PM</span></span></div> =0A=09<di=
v style=3D"margin:0px;padding:0px;"> =0A=09=09<span style=3D"font-family:Ve=
rdana;"><span style=3D"font-size:12px;">To: Manzetti, Sergio </span></span>=
</div> =0A=09<div style=3D"margin:0px;padding:0px;"> =0A=09=09<span style=
=3D"font-family:Verdana;"><span style=3D"font-size:12px;">Subject: CCL: Res=
onance energy</span></span></div> =0A=09<br> =0A=09<div> =0A=09=09<div> =0A=
=09=09=09<pre style=3D"white-space:pre-wrap;word-wrap:break-word;font-size:=
11;"> =0A&gt; Dear CCLrs, how can one extract the parameters of "resonance =
energy" =0A&gt; (Randic, 2003) from a SCF calculation of a neutral ring sys=
tem? =0A=0AOne cannot, in my opinion you need a vb code for that :) Have a =
look at Rashid =0Aet al. J. Phys. Chem. A 116, 4778-4788 (2012) [DOI 10.102=
1/jp211105t] =0ATry van Lenthe's from gamess(uk) or Cooper's SCVB from Molc=
as/Molpro. =0A=0ACheers, =0ARobert =0A=0A-- =0ARobert W. G=F3ra, Theoretica=
l Chemistry Group, ICHFiT, WUT [http://zcht.info] =0A[http://www.researchga=
te.net/profile/Robert_Gora] =0A[http://www.researcherid.com/rid/B-3919-2010=
]</pre> =0A=09=09</div> =0A=09</div> =0A</blockquote> =0A<div style=3D"marg=
in:0px;padding:0px;"> =0A=09&nbsp;</div> =0A<br> =0A</span></span>=0A</div>=
<meta http-equiv=3D"x-dns-prefetch-control" content=3D"on"><br><br> </div> =
</div>  </div></body></html>
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