From chemistry-request@ccl.net Wed Sep  1 10:21:15 2004
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From: Guosheng Wu <wu_guosheng2002=at=yahoo.com>
Subject: General scoring functions for PP, PL, and LL
To: chemistry=at=ccl.net
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Hi there,

In the computation of protein(P)-ligand(L) binding
free energy, one would like to have a quick and
accurate scoring function to evaluate all of those
non-bond interactions between atomic pairs of PP, PL,
and LL, for the strain energy of the target, binding
energy, and strain energy for ligand, respectively. So
that a more reasonable comparison with the
experimental activities can be justified.

However, things are often very complicated. It seems
most of current scoring functions are focused on the
PL part. For the LL part, simple energy difference
(between the solution state & binding state) from MM
is often claimed to be good enough. For the PP part,
it may be more difficult to quantify and validate, or
it simply adds more noise rather than useful
information. One may argue that the PL part is usually
the dominant component. Still it's not that simple in
many cases, otherwise, no one would really care about
the business of flexibility.

Does anyone notice any kind of "general" approach for
this task? Physically, should there be much difference
for these three kinds of potentials?

I would like to get your comments or reminding of
relevant literature. 

Thanks a lot. 

Guosheng

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From chemistry-request@ccl.net Wed Sep  1 01:44:28 2004
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From: "Raju Vishwanathan" <raju.v=at=sysarris.soft.net>
To: <CHEMISTRY=at=ccl.net>
Subject: Problem encountered in Marvin Editor
Date: Wed, 1 Sep 2004 12:22:46 +0530
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Hi CCL memebers,

I am working on 2D MDL Mol files.
My existing 2D Mol files were opened in Marvin Editor and again saved it as
(.MOL) file. Just curious enough to check the Mol structure file.
And to my surprise the Co-ordinates for the same structure has changed.
(Though the structure is the same). I repeated this for my all structures,
co-ordinates have changed.

Has anybody tried this and already reported. Please let me know.

I repeated this with all my 3D MDL Mol files. The same co-ordinate problem
is repeating! This has serious implications in 3D descriptors???
The 3D descriptor values no longer remain the same for the same structure.

I would be glad if you could give your comments and feedback to solve this
problem!!!!!!!


Thanking you,
Warm Regards,
Raju Vishwanathan
Sr. Consultant
SysArris Software
# 120 A, Elephant Rock Road,
III Block, Jayanagar,( Opp to HSBC ATM ).
Bangalore-560011
India.
Tel. No. 91-80-26654965,26655052,26642690,
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From chemistry-request@ccl.net Wed Sep  1 01:36:48 2004
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To: chemistry*at*ccl.net,
   "Computational Chemistry List" <chemistry-request*at*ccl.net>
Subject: Optical rotation computation?
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Dear Colleagues,

Which software can predict optical rotation of chiral molecules?

Regards,

Dr. Andras Borosy
Seniour Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz AG
Ueberlandstr. 138
8600 D|bendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy*at*givaudan.com



From chemistry-request@ccl.net Wed Sep  1 10:00:49 2004
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From: "Albena Jivkova Patleeva" <albena*at*shu-bg.net>
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Subject: CCL: resonance energy estimating
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Dear CCL's

=20

I need value of the resonance energy (IUPAC definition: The difference =
in potential energy between the actual molecular entity and the =
contributing structure of lowest potential energy) of selenophene and I =
have no an idea how to calculate it. I would appreciate if someone =
explains me how the resonance energy has to be estimated.=20

=20

Albena Patleeva

a.patleeva*at*shu-bg.net

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<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Dear =
CCL's</SPAN><?xml:namespace=20
prefix =3D o ns =3D "urn:schemas-microsoft-com:office:office" =
/><o:p></o:p></P>
<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><FONT size=3D3><FONT=20
face=3D"Times New Roman">&nbsp;<o:p></o:p></FONT></FONT></P>
<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">I need value of the =
resonance energy=20
(</SPAN><SPAN lang=3DEN-US=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: =
EN-US">IUPAC=20
definition: </SPAN><FONT face=3D"Times New Roman" size=3D3>The =
difference in=20
potential energy between the actual <SPAN=20
style=3D"mso-bidi-font-style: italic">molecular entity</SPAN> and the =
<SPAN=20
style=3D"mso-bidi-font-style: italic">contributing structure</SPAN> of =
lowest=20
potential energy</FONT><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
Arial">) of=20
selenophene&nbsp;and I </SPAN><SPAN lang=3DEN-US=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: =
EN-US">have no an=20
idea</SPAN><SPAN style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"> how to =
calculate=20
it</SPAN><SPAN lang=3DEN-US=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: =
EN-US">. I would=20
appreciate if someone explains&nbsp;me how the resonance energy has to =
be=20
estimated. </SPAN><o:p></o:p></P>
<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><FONT size=3D3><FONT=20
face=3D"Times New Roman">&nbsp;<SPAN lang=3DEN-US=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial; mso-ansi-language: =
EN-US"><o:p></o:p></SPAN></FONT></FONT></P>
<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Albena=20
Patleeva</SPAN><o:p></o:p></P>
<P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN=20
style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"><A=20
href=3D"mailto:a.patleeva*at*shu-bg.net">a.patleeva*at*shu-bg.net</A></SPAN><o:=
p></o:p></P></FONT></DIV></BODY></HTML>

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From chemistry-request@ccl.net Wed Sep  1 11:48:04 2004
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Date: Wed, 1 Sep 2004 09:57:15 -0700 (PDT)
From: "J. Zheng" <jzheng73(at)u.washington.edu>
To: chemistry(at)ccl.net
Subject: predict 3D structure from sequence
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hi, folks:

Do you know any software can predict 3D structure of protein according the
sequence of amino acid?

Jie

-----------------------------------------------
|  JIE ZHENG                          	      |
|  Graduate Student			      |
|  Department of Chemical Engineering	      |
|  University of Washington		      |
|  Seattle, WA 98105, USA   		      |
-----------------------------------------------
|  Tel:  (206) 529-1373 (h)		      |
|        (206) 616-6510 (o)		      |
| Email: jzheng73(at)u.washington.edu	      |
-----------------------------------------------


From chemistry-request@ccl.net Wed Sep  1 11:19:23 2004
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From: "Steve Bowlus" <chezbowlus-.at.-goldrush.com>
To: <Andras.Borosy-.at.-givaudan.com>, <chemistry-.at.-ccl.net>
Subject: RE: Optical rotation computation?
Date: Wed, 1 Sep 2004 09:28:31 -0700
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ADF from SCM (www.scm.com) has this capability.

sb

> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]On
> Behalf Of Andras.Borosy-.at.-givaudan.com
> Sent: Tuesday, August 31, 2004 11:33 PM
> To: chemistry-.at.-ccl.net; Computational Chemistry List
> Subject: CCL:Optical rotation computation?
> 
> 
> Dear Colleagues,
> 
> Which software can predict optical rotation of chiral molecules?
> 
> Regards,
> 
> Dr. Andras Borosy
> Seniour Scientist
> Delivery Systems, Fragrance Research
> Givaudan Schweiz AG
> Ueberlandstr. 138
> 8600 D|bendorf
> Switzerland
> tel: + 41-1-8242164
> fax: +41-1-8242926
> e-mail: andras.borosy-.at.-givaudan.com
> 
> 
> 
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