From chemistry-request@ccl.net Tue Apr 12 06:24:27 2005
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From: "Xavier" <xgallet~at~nautilusbiotech.com>
To: <chemistry~at~ccl.net>
Subject: CCL: atomic hydrophobicity
Date: Tue, 12 Apr 2005 11:02:14 +0200
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Dear CCLers,

Could someone provide me one or sevaral tables of atomic hydrophobicity (or
lipophilicity) values for each atom type. I know several tables are
described in papers from Crippen/Ghose, Fauchhre, Broto, etc... but most of
those articles are old and not available to me. Moreover, no such tables
seem to be available on the web.

Thank in advance,

Xavier GALLET




From chemistry-request@ccl.net Mon Apr 11 22:52:41 2005
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To: chemistry~at~ccl.net
From: Dave Winkler <dave.winkler~at~csiro.au>
Subject: Complex systems science and drug discovery at Pacifichem 2005
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Pacifichem 2005
Honolulu, Hawaii
December 15-20 2005
http://www.pacifichem.org

Abstract submissions close at COB 13 April US ET

Symposium on Complexity and other Computational Methods in Drug Design

This symposium, one of approximately 350 that=20
form the Pacifichem congress, explores how=20
complex systems science can provide an=20
alternative paradigm for understanding chemical=20
and biological systems relevant to drug design.=20
Papers submitted to date include...

John Finnigan (CSIRO, Australia) Complex Systems, Chemistry and Biology
David Winkler (CSIRO, Australia) Modelling=20
Emergent Properties Of Complex Biological And=20
Chemical Systems
Dimitris Agrafiotis (J&J, USA) A self-organizing=20
principle for modeling proximity data
Gerry Maggiora (Uni of Arizona, USA) Applications=20
of rough set theory in drug-discovery research
Bernard Testa (Uni Hospital Centre, Switzerland)=20
Computational explorations of the property space=20
of biomolecules
Tim Clark (Uni of Erlangen, Germany) Molecular=20
surface properties: What are they trying to tell=20
us?
=46rank Burden (Scimetrics, Australia) The=20
Application of Agent Based Modelling to Chemical=20
and Biological Problems
Tatsuya Takagi (Osaka Uni, Japan) Development of=20
a simple nonparametric regression method
Yuzong Chen (National Uni Singapore) Machine=20
Learning Methods in Facilitating the Prediction=20
of Drug ADME and Toxicological Properties
Monty Kier (Virginia Commonwealth Uni, USA) A=20
theory of ligand passage through hydrodynamic=20
chreodes modeled with cellular automata.
Val Gillett (Uni of Sheffield, UK) Application of=20
Multiobjective Evolutionary Optimisation=20
Techniques to Pharmacophore Identification
Tudor Oprea (Uni New Mexico, USA)	 Rapid=20
evaluation of synthetic and molecular complexity=20
for lead discovery
Martyn Ford (Portsmouth Uni, UK) Analysis of the=20
Molecular Dynamics of Simple and Complex Systems=20
for Predictive Biology
John Gasteiger (Uni of Erlangen, Germany)=20
Analyzing Biochemical Pathways by Neural Networks=20
and Genetic Algorithms
Jean-Fran=E7ois Truchon (Merck, Canada) Designing=20
good combinatorial libraries: throwing out the=20
trash instead of sorting through the trash
Peter Stadler (Leipzig Uni, Germany) Generalized=20
Topological Spaces in Evolutionary Theory and=20
Combinatorial Chemistry
Nigel Richards (Uni of Florida, USA)=20
Structure-based discovery of asparagine=20
synthetase inhibitors as agents for the clinical=20
treatment of asparaginase-resistant leukemias
Greg Dewey (Keck Inst) Complexity in biology
Hideaki Suzuki Biologically-mimetic computing
Yuan-Ping Pang (Mayo Clinic) Holistic approach to=20
small-molecule inhibitors of the zinc=20
endopeptidase of botulinum neurotoxin serotype A
Max Dang (Metabasis Therapeutics, USA) Discovery=20
of FBPase inhibitors using a rational drug design
Arvydas Tamulis (Vilnius University, Lithuania)=20
Quantum Mechanical Modeling of Self-Reproducible=20
Living PNA Chip Immersed in the Lipid Bilayer=20
Vesicle Controlled by Quantum Computing Logic=20
Gates
Mitch Polley (CSIRO, Australia) Virtual Library=20
Design of Drug-Like Molecules Using Evolutionary=20
Methods and Compound Fitness Functions
Seymour B. Elk (Elk Tech Assoc. USA) Chemical=20
simplexes - a function of dimension developing a=20
more efficient system of taxonomy and nomenclature
Julianne Halley (Monash Uni, Australia)=20
Self-organization as a source of collective=20
intelligence
Darryl Jones (Flinders Uni, Australia) Momentum=20
Space Descriptors for Quantitative=20
Structure-Activity Relationships
Kato, Hiroaki (Toyohashi Uni Technology, Japan)=20
Three-dimensional protein structural data mining=20
based on the glycine filter reduced representation
Stefano Moro (Uni Padova, Italy)) Integrated=20
ligand and receptor-based strategies to discover=20
new GPCR ligands: the human A3 adenosine receptor=20
as a key study.
Sergey Bachurin (Inst Physiolog Active Compounds,=20
Russia) Computational approaches to synthetic=20
design, discovery and development of new=20
neuroactive glutamate receptor ligands
Hiroshi Chuman (Toyohashi Uni Technology, Japan)=20
Connecting Traditional QSAR and Molecular=20
Simulations - Structure Based Quantitative=20
Structure-Activity Relationship of Papain and=20
HIV-1-Protease Inhibitors

--
Cheers,
Dave

Dr. David A. Winkler FRACI CChem CPChem	Email: dave.winkler~at~csiro.au  
CSIRO Centre for Complexity in Drug Design	Voice: 61-3-9545-2477
Senior Principal Research Scientist    		Fax:  61-3-9545-2561
CSIRO Molecular Science		                  or 61-3-9545-2446
Private Bag 10,Clayton South MDC 3169 	http://www.csiro.au
Australia	       				http://www.molsci.csiro.au

Join us at CONNECT2005=20
(http://www.pco.com.au/connect2005/) 3-7 July=20
2005, the Royal Australian Chemical Institute's=20
National Convention, the 11th Asian Chemical=20
Congress in Seoul, August 24-26 2005=20
(http://www.11acc.org/), and Pacifichem 2005 in=20
Honolulu December 15-20=20
(http://www.pacifichem.org).

-- 
Cheers,
Dave

Dr. David A. Winkler FRACI CChem CPChem	Email: dave.winkler~at~csiro.au  
CSIRO Centre for Complexity in Drug Design	Voice: 61-3-9545-2477
Senior Principal Research Scientist    		Fax:  61-3-9545-2561
CSIRO Molecular Science		                  or 61-3-9545-2446
Private Bag 10,Clayton South MDC 3169 	http://www.csiro.au
Australia	       				http://www.molsci.csiro.au

Join us at CONNECT2005=20
(http://www.pco.com.au/connect2005/) 3-7 July=20
2005, the Royal Australian Chemical Institute's=20
National Convention, the 11th Asian Chemical=20
Congress in Seoul, August 24-26 2005=20
(http://www.11acc.org/), and Pacifichem 2005 in=20
Honolulu December 15-20=20
(http://www.pacifichem.org).
--============_-1098853603==_ma============
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type=3D"text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
 --></style><title>Complex systems science and drug discovery at
Pacifichem 2</title></head><body>
<div><br></div>
<div align=3D"center"><b>Pacifichem 2005</b></div>
<div align=3D"center"><b>Honolulu, Hawaii</b></div>
<div align=3D"center"><b>December 15-20 2005</b></div>
<div align=3D"center"><b>http://www.pacifichem.org</b></div>
<div align=3D"center"><b><br></b></div>
<div align=3D"center"><font color=3D"#FF0000"><b>Abstract submissions
close at COB 13 April US ET</b></font></div>
<div><br></div>
<div><i>Symposium on Complexity and other Computational Methods in
Drug Design</i></div>
<div><br></div>
<div>This symposium, one of approximately 350 that form the Pacifichem
congress, explores how complex systems science can provide an
alternative paradigm for understanding chemical and biological systems
relevant to drug design.&nbsp; Papers submitted to date
include...</div>
<div><font color=3D"#000000"><br></font></div>
<ul>
<li><font color=3D"#000000">John Finnigan (CSIRO, Australia)<i> Complex
Systems, Chemistry and Biology</i>
<li>David Winkler (CSIRO, Australia)<i> Modelling Emergent Properties
Of Complex Biological And Chemical Systems</i>
<li>Dimitris Agrafiotis (J&amp;J, USA)<i> A self-organizing principle
for modeling proximity data</i>
<li>Gerry Maggiora (Uni of Arizona, USA)<i> Applications of rough set
theory in drug-discovery research</i>
<li>Bernard Testa (Uni Hospital Centre, Switzerland)<i> Computational
explorations of the property space of biomolecules</i>
<li>Tim Clark (Uni of Erlangen, Germany)<i> Molecular surface
properties: What are they trying to tell us?</i>
<li>Frank Burden (Scimetrics, Australia)<i> The Application of Agent
Based Modelling to Chemical and Biological Problems</i>
<li>Tatsuya Takagi (Osaka Uni, Japan)<i> Development of a simple
nonparametric regression method</i>
<li>Yuzong Chen (National Uni Singapore)<i> Machine Learning Methods
in Facilitating the Prediction of Drug ADME and Toxicological
Properties</i>
<li>Monty Kier (Virginia Commonwealth Uni, USA)<i> A theory of ligand
passage through hydrodynamic chreodes modeled with cellular
automata</i>.
<li>Val Gillett (Uni of Sheffield, UK)<i> Application of
Multiobjective Evolutionary Optimisation Techniques to Pharmacophore
Identification</i>
<li>Tudor Oprea (Uni New Mexico,
USA)<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab><i> Rapid
evaluation of synthetic and molecular complexity for lead
discovery</i>
<li>Martyn Ford (Portsmouth Uni, UK)<i> Analysis of the Molecular
Dynamics of Simple and Complex Systems for Predictive Biology</i>
<li>John Gasteiger (Uni of Erlangen, Germany)<i> Analyzing Biochemical
Pathways by Neural Networks and Genetic Algorithms</i>
<li>Jean-Fran=E7ois Truchon (Merck, Canada)<i> Designing good
combinatorial libraries: throwing out the trash instead of sorting
through the trash</i>
<li>Peter Stadler (Leipzig Uni, Germany)<i> Generalized Topological
Spaces in Evolutionary Theory and Combinatorial Chemistry</i>
<li>Nigel Richards (Uni of Florida, USA)<i> Structure-based discovery
of asparagine synthetase inhibitors as agents for the clinical
treatment of asparaginase-resistant leukemias</i>
<li>Greg Dewey (Keck Inst)<i> Complexity in biology</i>
<li>Hideaki Suzuki<i> Biologically-mimetic computing</i>
<li>Yuan-Ping Pang (Mayo Clinic)<i> Holistic approach to
small-molecule inhibitors of the zinc endopeptidase of botulinum
neurotoxin serotype A</i>
<li>Max Dang (Metabasis Therapeutics, USA)<i> Discovery of FBPase
inhibitors using a rational drug design</i>
<li>Arvydas Tamulis (Vilnius University, Lithuania)<i> Quantum
Mechanical Modeling of Self-Reproducible Living PNA Chip Immersed in
the Lipid Bilayer Vesicle Controlled by Quantum Computing Logic
Gates</i>
<li>Mitch Polley (CSIRO, Australia)<i> Virtual Library Design of
Drug-Like Molecules Using Evolutionary Methods and Compound Fitness
=46unctions</i>
<li>Seymour B. Elk (Elk Tech Assoc. USA)<i> Chemical simplexes - a
function of dimension developing a more efficient system of taxonomy
and nomenclature</i>
<li>Julianne Halley (Monash Uni, Australia)<i> Self-organization as a
source of collective intelligence</i>
<li>Darryl Jones (Flinders Uni, Australia)<i> Momentum Space
Descriptors for Quantitative Structure-Activity Relationships</i>
<li>Kato, Hiroaki (Toyohashi Uni Technology, Japan)<i>
Three-dimensional protein structural data mining based on the glycine
filter reduced representation</i>
<li>Stefano Moro (Uni Padova, Italy))<i> Integrated ligand and
receptor-based strategies to discover new GPCR ligands: the human A3
adenosine receptor as a key study</i>.
<li>Sergey Bachurin (Inst Physiolog Active Compounds, Russia)<i>
Computational approaches to synthetic design, discovery and
development of new neuroactive glutamate receptor ligands</i>
<li>Hiroshi Chuman (Toyohashi Uni Technology, Japan)<i> Connecting
Traditional QSAR and Molecular Simulations - Structure Based
Quantitative Structure-Activity Relationship of Papain and
HIV-1-Protease Inhibitors</i></font></ul>
<div><br></div>
<div><tt>--</tt></div>
<div>Cheers,<br>
Dave<br>
<br>
Dr. David A. Winkler FRACI CChem
CPChem<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Email:
dave.winkler~at~csiro.au&nbsp;&nbsp;<br>
CSIRO Centre for Complexity in Drug
Design<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Voice:
61-3-9545-2477<br>
Senior Principal Research
Scientist&nbsp;&nbsp;&nbsp;&nbsp;<x-tab>&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>Fax:&nbsp; 61-3-9545-2561<br>
CSIRO Molecular Science<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab
>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span
></span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; or 61-3-9545-2446<br>
Private Bag 10,Clayton South MDC
3169&nbsp;<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>http://www.csiro.au<br>
Australia<x-tab>&nbsp;&nbsp;&nbsp;
</x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<x-tab>
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>http://www.molsci.csiro.au<br>
<br>
Join us at CONNECT2005 (http://www.pco.com.au/connect2005/) 3-7 July
2005, the Royal Australian Chemical Institute's National Convention,
the 11th Asian Chemical Congress in Seoul, August 24-26 2005
(http://www.11acc.org/), and Pacifichem 2005 in Honolulu December
15-20 (http://www.pacifichem.org).</div>
<div><br></div>
<x-sigsep><pre>-- 
</pre></x-sigsep>
<div>Cheers,<br>
Dave<br>
<br>
Dr. David A. Winkler FRACI CChem
CPChem<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Email:
dave.winkler~at~csiro.au&nbsp;&nbsp;<br>
CSIRO Centre for Complexity in Drug
Design<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </x-tab>Voice:
61-3-9545-2477<br>
Senior Principal Research
Scientist&nbsp;&nbsp;&nbsp;&nbsp;<x-tab>&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>Fax:&nbsp; 61-3-9545-2561<br>
CSIRO Molecular Science<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab
>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span
></span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; or 61-3-9545-2446<br>
Private Bag 10,Clayton South MDC
3169&nbsp;<x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>http://www.csiro.au<br>
Australia<x-tab>&nbsp;&nbsp;&nbsp;
</x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<x-tab>
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab><x-tab>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</x-tab>http://www.molsci.csiro.au<br>
<br>
Join us at CONNECT2005 (http://www.pco.com.au/connect2005/) 3-7 July
2005, the Royal Australian Chemical Institute's National Convention,
the 11th Asian Chemical Congress in Seoul, August 24-26 2005
(http://www.11acc.org/), and Pacifichem 2005 in Honolulu December
15-20 (http://www.pacifichem.org).</div>
</body>
</html>
--============_-1098853603==_ma============--


From chemistry-request@ccl.net Tue Apr 12 05:09:12 2005
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Dear All,

We would like to obtain geometry structure of several organic compounds in the acetonitrile solvent applying GAMESS package. We must give the following numerical values of acetonitrile:
1. The radius in Angstrom
2. The dielectric constant 
3. The dielectric costant at infinite frequency 
4. The thermal expansion coefficient (1/K) 
5. Molar volume (ml/mol) of acetonitrile
6. The surface tension (dyne/cm)
7. The thermal coefficient of log(surface tension)
8.  The cavity microscopic coeficient 

It will be very kind of you to help us to find the above mentioned munerical values of acetonitrile.

Thank you in advance.

With respect,

Elena


From chemistry-request@ccl.net Tue Apr 12 09:06:59 2005
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From: "Corinne, , DUFAURE" <corinne_dufaure|at|yahoo.fr>
To: chemistry|at|ccl.net
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Subject: W:DOS
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hello everybody,
who can help me to draw the density of states of a cluster?
I know about the theory but I have a problem to do it in practise : which software...

thanks.
C.



From chemistry-request@ccl.net Tue Apr 12 11:40:17 2005
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Date: Tue, 12 Apr 2005 07:40:43 -0700 (PDT)
From: "S.I.Gorelsky" <gorelsky !! stanford.edu>
To: "Corinne, , DUFAURE" <corinne_dufaure !! yahoo.fr>
cc: chemistry !! ccl.net
Subject: Re: CCL:W:DOS
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Check http://www.sg-chem.net

AOMix can generate the DOS plot data from numerous quantum-chemistry
packages.

Best regards,

Serge Gorelsky

On Tue, 12 Apr 2005, Corinne, , DUFAURE wrote:

> hello everybody,
> who can help me to draw the density of states of a cluster?
> I know about the theory but I have a problem to do it in practise : which software...
>
> thanks.
> C.
>
>
>
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----------------------------------------------------------------
 Dr S.I. Gorelsky, Department of Chemistry, Stanford University
 Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
 Phone: (650) 723-0041. Fax: (650) 723-0852.
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From chemistry-request@ccl.net Tue Apr 12 11:57:08 2005
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Subject: Re: CCL:W:DOS
From: "Noel O'Boyle" <noel.oboyle2 _(a)_ mail.dcu.ie>
To: "Corinne, , DUFAURE" <corinne_dufaure _(a)_ yahoo.fr>
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What program are you using to do the cluster calculation? If it's
Gaussian or GAMESS you can use http://gausssum.sf.net.

Otherwise you may have luck with http://www.sg-chem.net/aomix/.

Noel

On Tue, 2005-04-12 at 14:06, Corinne, , DUFAURE wrote:
> hello everybody,
> who can help me to draw the density of states of a cluster?
> I know about the theory but I have a problem to do it in practise : which software...
> 
> thanks.
> C.
> 
> 
> 
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From chemistry-request@ccl.net Tue Apr 12 17:54:48 2005
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Subject: W:CALL FOR PAPERS, ACS: "ADVANCES IN DATA MINING AND ANALYSIS"
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Call for Papers - 230th ACS National Meeting, Washington, DC (August 28-September 1, 2005)

ADVANCES IN DATA MINING AND ANALYSIS  COMPUTATIONAL PERSPECTIVE
Sponsored by Computers in Chemistry Division (COMP)
Co-sponsored by Chemical Information Division (CINF)

and

ADVANCES IN DATA MINING AND ANALYSIS  INFORMATICS PERSPECTIVE
Sponsored by CINF
Co-sponsored by COMP

We invite you to submit abstracts for the symposium entitled Advances in Data Mining and Analysis at the upcoming ACS National Meeting at Washington D.C.  Jointly organized by CINF and COMP, the symposium will cover issues and opportunities from both computational and informatics perspectives

If you have views on data mining methodologies, new algorithms, data analysis and visualization, data pipelining and workflows, consider submitting abstract to the COMP symposium.  

Those who could share their perspectives on chemical databases, database searching, and hit list management, scientific text mining, IP-based data mining and competitive intelligence, knowledge capture and management, virtual collaboratories, consider submitting abstract to the CINF symposium

Additional topics are also welcome.

Please use the on-line abstract submission system (OASYS) for submitting your abstract (http://oasys.acs.org/oasys.htm):  Select the CINF or COMP Division depending on your topic of interest.  The system will take you through 5 easy steps to submit your abstract.  The deadline for submitting abstracts is April 25, 2005 for COMP and May 3, 2005 for CINF. 

Symposium organizers: Alex Tropsha (alex_tropsha _()_ unc.edu) and Osman Guner (osman _()_ accelrys.com).



