From chemistry-request@ccl.net Wed Sep 29 07:51:33 2004
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Subject: CCL: advice requested regarding overlay software
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Enzyme crystal structures lack hydrogens and usually contain inhibitors.  Due 
to the size of the crystal structures computing at a high level of theory with 
different substrates is not feasible.  It is our hope to be able to compute 
fragments of the active site at high level of theory and combine them to a 
realistic model.  Is there a program which allows overlaying computed 
geometries and experimental crystal structures using least squares fitting?  
Any advice on how to compare computed with experimental to ensure maximum 
overlap of the combined optimized fragments to the entire crystal.  Is there a 
way to ensure the orientation of the fragments as they would be in the crystal?

Any advice would be greatly appreciated.

Ken Hunter
Mount Allison University

From chemistry-request@ccl.net Wed Sep 29 07:42:15 2004
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From: Stephen Bowlus <chezbowlus<<at>>goldrush.com>
Subject: Re: CCL:mutant proteins....
Date: Wed, 29 Sep 2004 05:50:51 -0700
To: "Dimitrios Vlachakis" <VlachakisD1<<at>>cardiff.ac.uk>
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A free minimizer for proteins is TINKER from the Jay Ponder group at  
WashU.  It has among others an AMBER FF (or should I say a Kollman FF?)  
implementation, with several of the published parameter sets.  Beware:   
The translation from the working TINKER xyz format back to a fully  
informative pdb format can be painful if you have limited scripting  
skills.

Steve Bowlus


On Sep 28, 2004, at 2:55 PM, Dimitrios Vlachakis wrote:

> ** High Priority **
>
> Dear Holly,
>
> first of all I will asume that you are looking for some freeware. The  
> most user
> friendly (in terms of installation and actually using the software is  
> the Deep
> View
> Swiss-PdbViewer. It runs for all major platforms (mac 9&10, windows,  
> linux and
> iris) and installing it just involves hitting the Ok button a few  
> times. All you
> have to do then is to load your protein.pdb file, select the amino  
> acid you want
> to mutate and mutate to another on from a list (all with the mouse).
>
> The software can be found here:                 
> http://www.expasy.org/spdbv/
> And a tutorial on protein mutation here:
> http://www.expasy.org/spdbv/text/mutation.htm
>
>
> A quick comment though: I do not think it is very wise to do mutate  
> amino acids
> in a protein using freeware. And there is nothing wrong with freeware,  
> but it is
> not up to the job (most of the times). Mutating an amino acid with any  
> piece of
> software involves the substitution of the original side chain of the  
> aa with the
> one of the new aa. That is quite easy to do and is the easiest part of  
> the whole
> mutation job. The problem is how viable and realistic and mutant  
> protein is. The
> only way to fix that is to minimise energetically the protein, so that  
> the
> energy will drop and the protein will adopt a more stable  
> conformation. Now,
> doing that with freeware is simply IMPOSSIBLE! Deep View has  
> implemented a
> minimisation algorithm, but it is very poor especailly when dealing  
> with
> proteins. It uses the GROMOS 43B1 force field that is only good enough  
> to make
> room for new (potentially larger) amino acids. So, it will get stuck  
> in a local
> minima as it it will not be able to by pass through high energy  
> barriers. So, i
> suggest, that you should either get your hands on a decent software  
> package that
> can do both mutating and minimising in a proper scientific way (such  
> as Sybyl,
> Moe, hyperchem etc) or if you are going to use freeware to do the  
> mutating part
> (such as Deep Blue) find a reliable minimising package. a 30 day  
> evaluation of
> hyperchem is available from here: (http://www.hyper.com)
>
> Hope that helps,
>
>
>
>
> Dimitrios Vlachakis
> PhD student in Molecular Modelling
> Medicinal Chemistry Group
> Welsh School of Pharmacy
> Cardiff University
>
> Redwood Building
> King Edward VII Avenue
> CF10 3XF
> Cardiff
> Wales, UK
>
> tel. +44 2920 877221
> tel. +44 2920 874551 (lab)
> fax. +44 2920 874537
>
>> ...................................................................... 
>> .............
>
>
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>
>



From chemistry-request@ccl.net Wed Sep 29 03:39:29 2004
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From: Jamie Platts <Platts[at]Cardiff.ac.uk>
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To: Torben Rasmussen <Torben.Rasmussen[at]kemi.uu.se>
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Subject: Re: CCL:Hydrophobic surface area
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  Dear Torben,

  I can send a copy of Dodd and Theorodou's original VOLUME program, which
treats molecules as a set of super-imposed vdw spheres and reports their
exposed surface area (see reference below).

  We've also modified this to read MDL mol files, and automatically
identify polar (N, O, NH, OH) atoms, if this would be useful. Both are
freely distributed under the GNU GPL.

  Hope this helps. Cheers,

  Jamie

C---------------------------------------------------------------------C
C     Reference:                                                      C
C                                                                     C
C       "Analytical treatment of the volume and surface area of       C
C       molecules formed by an arbitrary collection of unequal        C
C       spheres intersected by planes"                                C
C                                                                     C
C     L.R. Dodd and D.N. Theodorou                                    C
C     MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991   C
C---------------------------------------------------------------------C

----------------------------------------------------------
  Jamie Platts
  School of Chemistry  		Phone: +44 (0) 2920 874950
  Cardiff University 	 	Email: platts[at]cf.ac.uk
  P.O. Box 912 			FAX:   +44 (0) 2920 874030
  Cardiff CF10 3TB 		www.cf.ac.uk/chemy

> Hi,
>
> I am looking for programs/algorithms/approaches to evaluate hydrophobic
> surface AND surface area for, primarily, organic molecules. Both free
> and commercial programs, suitable for a small research budget, are of
> interest. Pointers to literature discussing this subject will also be
> most appreciated!
>
> I will summarize to the list.
>
> Thanks!
> Torben.
>
> --
> Torben Rasmussen
> Uppsala University
> Department of Organic Chemistry
> E-mail: Torben.Rasmussen[at]kemi.uu.se
>
>
>
> -= This is automatically added to each message by the mailing script =-
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>
>
>
>
>
>


From chemistry-request@ccl.net Wed Sep 29 08:38:14 2004
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Subject: CCL: Ligand Alignment to Experimentally Derived Structres
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Greetings to all,
=20
I would like to ask your help in finding pertinent recent papers on the =
use of alignment algorithms for ligand-based drug design approaches. In =
this vein, any paper involving flexible/rigid alignment of unknowns to =
an experimentally determined structure (i.e.: NMR or X-Ray) is =
sought-after. Both successful and unsuccessful results are appreciated, =
as well as reviews.
=20
Personal comments and opinions are also welcomed.
Thank you for your cooperation,
=20
APM
=20

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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Greetings to all,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>I would like to ask your help in finding pertinent =
recent papers
on the use of alignment algorithms for <span =
class=3DSpellE>ligand</span>-based
drug design approaches. In this vein, any paper involving flexible/rigid =
alignment
of unknowns to an experimentally determined structure (i.e.: NMR or =
X-Ray) is sought-after.
Both successful and unsuccessful results are appreciated, as well as =
reviews.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Personal comments and opinions are also =
welcomed.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thank you for your =
cooperation,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>APM<o:p></o:p></span></font></p>

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style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

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From chemistry-request@ccl.net Wed Sep 29 03:36:15 2004
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From: "Jens Spanget-Larsen" <spanget|at|virgil.ruc.dk>
Organization: Roskilde Universitetscenter
To: Hans Martin Senn <senn|at|mpi-muelheim.mpg.de>
Date: Wed, 29 Sep 2004 10:46:48 +0200
Subject: Re: CCL:Origin of dipole moment in Gaussian
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Dear Hans Martin,

according to the manuals, output controlled by the POP 
keyword, including dipole and multipole moments, is expressed 
in the coordinate system defined by the 'standard 
orientation'. The origin of this system is the center of 
nuclear charge (presumably because this simplifies the 
evaluation of multipole terms). The orientation of the 
coordinate axes is determined by the molecular symmetry 
elements, if present.  

Jens >--<

> Dear all
> 
> This question is almost embarrassing, but I was unable to find a  
> definite statement as to the choice of origin of the dipole moment in  
> Gaussian 03's output. I have come across hints for both the centre of  
> mass and the centre of nuclear charges. Can anybody provide me with an  
> authoritative answer?
> 
> Best regards
> 
> Hans



=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
JENS SPANGET-LARSEN         Office:         +45 4674 2710
Department of Chemistry     Fax:            +45 4674 3011
Roskilde University (RUC)   Mobile:         +45 2320 6246
P.O.Box 260                 E-Mail:        spanget|at|ruc.dk
DK-4000 Roskilde, Denmark   http://virgil.ruc.dk/~spanget
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From chemistry-request@ccl.net Wed Sep 29 08:37:34 2004
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Subject: Fwd: CCL:mutant proteins....
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My bad!!

Please disregard the wholly undeserved slur on Ponder's xyzpdb program 
I posted a few minutes ago.  Wonderful program that does exactly what 
is needed, if you have both the .xyz and .seq files correctly defined 
for the desired output!

sb

Begin forwarded message:

> From: Stephen Bowlus <chezbowlus{at}goldrush.com>
> Date: September 29, 2004 5:50:51 AM PDT
> To: "Dimitrios Vlachakis" <VlachakisD1{at}cardiff.ac.uk>
> Cc: <CHEMISTRY{at}ccl.net>
> Subject: Re: CCL:mutant proteins....
>
> A free minimizer for proteins is TINKER from the Jay Ponder group at 
> WashU.  It has among others an AMBER FF (or should I say a Kollman 
> FF?) implementation, with several of the published parameter sets.  
> Beware:  The translation from the working TINKER xyz format back to a 
> fully informative pdb format can be painful if you have limited 
> scripting skills.
>
> Steve Bowlus
>

--Apple-Mail-1-46786951
Content-Transfer-Encoding: 7bit
Content-Type: text/enriched;
	charset=US-ASCII

My bad!!


Please disregard the wholly undeserved slur on Ponder's xyzpdb program
I posted a few minutes ago.  Wonderful program that does exactly what
is needed, if you have both the .xyz and .seq files correctly defined
for the desired output!


sb


Begin forwarded message:


<excerpt><bold><color><param>0000,0000,0000</param>From:
</color></bold>Stephen Bowlus <<chezbowlus{at}goldrush.com>

<bold><color><param>0000,0000,0000</param>Date:
</color></bold>September 29, 2004 5:50:51 AM PDT

<bold><color><param>0000,0000,0000</param>To:
</color></bold>"Dimitrios Vlachakis" <<VlachakisD1{at}cardiff.ac.uk>

<bold><color><param>0000,0000,0000</param>Cc:
</color></bold><<CHEMISTRY{at}ccl.net>

<bold><color><param>0000,0000,0000</param>Subject: </color>Re:
CCL:mutant proteins....

</bold>

A free minimizer for proteins is TINKER from the Jay Ponder group at
WashU.  It has among others an AMBER FF (or should I say a Kollman
FF?) implementation, with several of the published parameter sets. 
Beware:  The translation from the working TINKER xyz format back to a
fully informative pdb format can be painful if you have limited
scripting skills.


Steve Bowlus


</excerpt>
--Apple-Mail-1-46786951--



From chemistry-request@ccl.net Wed Sep 29 11:22:42 2004
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Date: Wed, 29 Sep 2004 09:33:35 -0700 (PDT)
From: Vincent Xianlong Wang <xloongw_at_yahoo.com>
Subject: CCL: Energy accuracy for conformation calculation in Gaussian
To: CHEMISTRY_at_ccl.net
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Dear CCLer,

The accuracies of model chemistries in Gaussian have
been discussed in 'Exploring Chemistry with Electronic
Structure Methods' by J.B. Foresman et al. I'm
wondering if the energy accuracy could go higher in
the calculation for the energy difference among
different conformers of certain molecule? 
Your comments and reference information are welcome#!

Vincent



		
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From chemistry-request@ccl.net Wed Sep 29 04:08:14 2004
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Date: Wed, 29 Sep 2004 11:18:59 +0200 (MEST)
From: Michel Petitjean <ptitjean/at/itodys.jussieu.fr>
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Subject: CCL: Re: aligning structures via vector products - any good methods?
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To: chemistry/at/ccl.net
Subj: CCL: Re: aligning structures via vector products - any good methods?

What is m_i ? I assume that each quantity m_i (r_1i) is read
as a modified (r_1i). I assume also that the translation is fixed.
This is a constrained minimization problem: The unknown is the unit
quaternion minimizing the squared 2-norm of: \sum_i m_i (r_1i x r_2i).
The existence and unicity of the solution(s) have to be examined.
I do not exclude that there is an analytic solution, as for the
sum of squares method. Here the quaternionic solution is the simplest.
See: http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html
(and references herein) and the associated freewares ARMS and CSR:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.

Michel Petitjean,                     Email: petitjean/at/itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean/at/ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

Konstantin Kudin <konstantin_kudin/at/yahoo.com> wrote:
> Hi there,
>
 >I would like to align 2 structures via rotating one of them such that
> the sum of vector products between them is 0. More specifically:
>
>\sum_i m_i (r_1i x r_2i) = 0
>
 >Does anyone know of a good method that does that?
>
> Thanks!
> Kostya
>
>P.S. 
>
>One can also align things via list squares fit by minimizing
>{\sum_i m_i |r_1i - r_2i|^2}, but this is not what I need. The
>reference for this method is:
>S. K.Kearsley, Acta Cryst.  A45, 208 (1989).
>http://www.ccl.net/cca/software/SOURCES/FORTRAN/fitest/index.shtml



From chemistry-request@ccl.net Wed Sep 29 13:33:09 2004
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Date: Wed, 29 Sep 2004 15:43:30 -0300
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Subject: CCL: question about AMBER atom definition
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Our research group has been having some difficulties with atom definitions for 
AMBER files generated from GaussView 3.09.  For example C8 in purines should 
be a CK atom type but GaussView is defining it as CM.  There must be a program 
that defines it properly based on the usage of AMBER, or do most assign atom 
types manually?

Any assistance would be appreciated.

Ken Hunter
Mount Allison University


From chemistry-request@ccl.net Wed Sep 29 12:23:16 2004
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Message-ID: <415AF209.1060506(at)u.washington.edu>
Date: Wed, 29 Sep 2004 10:34:01 -0700
From: Oliver Hucke <ohucke(at)u.washington.edu>
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Holly,

another free program that can be used for mutating single residues is 
MODELLER (http://salilab.org/modeller/modeller.html). This is a full 
homology modeling program suite. The standard optimizing protocol 
employs simulated annealing which avoids the "local minimum problem" 
that Dimitrios pointed out. And the output is a proper pdb file - no 
scripting required. It takes a little while to learn the program though.

Best regards,
Oliver

-- 
________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center   Health Sciences Building - K418C
Dept. of Biochemistry           1959 NE Pacific St.
University of Washington        phone: (206) 685 7046
Box 357742                      fax  : (206) 685 7002
Seattle, WA 98195-7742          email: ohucke(at)u.washington.edu
________________________________________________________________

A free minimizer for proteins is TINKER from the Jay Ponder group at 
WashU.  It has among others an AMBER FF (or should I say a Kollman FF?) 
  implementation, with several of the published parameter sets.  Beware: 
   The translation from the working TINKER xyz format back to a fully 
informative pdb format can be painful if you have limited scripting  skills.

Steve Bowlus


On Sep 28, 2004, at 2:55 PM, Dimitrios Vlachakis wrote:

** High Priority **

Dear Holly,

first of all I will asume that you are looking for some freeware. The 
most user
friendly (in terms of installation and actually using the software is 
the Deep
View
Swiss-PdbViewer. It runs for all major platforms (mac 9&10, windows, 
linux and
iris) and installing it just involves hitting the Ok button a few 
times. All you
have to do then is to load your protein.pdb file, select the amino  acid 
you want
to mutate and mutate to another on from a list (all with the mouse).

The software can be found here:                 http://www.expasy.org/spdbv/
And a tutorial on protein mutation here:
http://www.expasy.org/spdbv/text/mutation.htm


A quick comment though: I do not think it is very wise to do mutate 
amino acids
in a protein using freeware. And there is nothing wrong with freeware, 
but it is
not up to the job (most of the times). Mutating an amino acid with any 
piece of
software involves the substitution of the original side chain of the  aa 
with the
one of the new aa. That is quite easy to do and is the easiest part of 
the whole
mutation job. The problem is how viable and realistic and mutant 
protein is. The
only way to fix that is to minimise energetically the protein, so that  the
energy will drop and the protein will adopt a more stable  conformation. 
Now,
doing that with freeware is simply IMPOSSIBLE! Deep View has  implemented a
minimisation algorithm, but it is very poor especailly when dealing  with
proteins. It uses the GROMOS 43B1 force field that is only good enough 
to make
room for new (potentially larger) amino acids. So, it will get stuck  in 
a local
minima as it it will not be able to by pass through high energy 
barriers. So, i
suggest, that you should either get your hands on a decent software 
package that
can do both mutating and minimising in a proper scientific way (such  as 
Sybyl,
Moe, hyperchem etc) or if you are going to use freeware to do the 
mutating part
(such as Deep Blue) find a reliable minimising package. a 30 day 
evaluation of
hyperchem is available from here: (http://www.hyper.com)

Hope that helps,




Dimitrios Vlachakis
PhD student in Molecular Modelling
Medicinal Chemistry Group
Welsh School of Pharmacy
Cardiff University

Redwood Building
King Edward VII Avenue
CF10 3XF
Cardiff
Wales, UK

tel. +44 2920 877221
tel. +44 2920 874551 (lab)
fax. +44 2920 874537

...................................................................... 
.............


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From chemistry-request@ccl.net Wed Sep 29 11:46:03 2004
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Date: Wed, 29 Sep 2004 19:02:06 +0200
From: Gabriele Cruciani <gabri.-at-.chemiome.chm.unipg.it>
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Hi Torben
try GRID, with DRY (hydrophobic) probe, for small molecules and 
biomolecules as well.
It is free. Windows UNIX and Linux are available, under www.moldiscovery.com

Gabriele Cruciani