From chemistry-request@server.ccl.net  Tue May  9 15:09:37 2000
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To: Steve Williams <willsd@conrad.appstate.edu>
cc: CHEMISTRY@ccl.net, jkerk@arnold.chem.uoa.gr
Subject: Re: CCL:estimate FP operations in Comp Chem (summary) 
In-Reply-To: Your message of "Tue, 09 May 2000 10:36:03 EDT."
             <3.0.32.20000509103603.00a99ac0@pop.appstate.edu> 
Date: Tue, 09 May 2000 12:09:29 -0700
From: David Konerding <dek@konerding.com>

Steve Williams writes:
>I apologize to those select ccl readers who have been waiting for this
>summary with bated breath; it is late but it is here:
>
>> 
>> As an example, a 1 teraflop machine, running for 5 years, nonstop, will
>> have done something on the order of 1E20 floating point operations, or
>> about 1/6000 of a mole.  
>> 
>
>i suspect it may be several moles, and following conventional
>wisdom on the rate of progress of computer hardware, as much
>will be computed in the next 2 years as in all of history before.
>the new super computers are almost scarry, a cray T3E maxed
>out can do over 2.4 GIGAflops/s!  is there anything that won't be
>calculable soon?  see:
><http://www.sgi.com/t3e/tech_info.html>
>i'd be fascinating if anyone has any pricing info on these systems,
>or other current crays, they are currently producing 4 product lines.
>it's simply fascinating.  The available processing power should
>continue to double every 2 years.

Yes, there's a lot that's incalculable today and will be so for the
forseeable future.  For example, calculating the full quantum equation
for the entire universe, or just brute-force cracking 1024-bit encryption,
would take you far longer than the life of the whole universe, and would
require more energy than the universe has to offer you.

Furthermore, you should be aware that the T3E is basically an obsolete
machine and that very few people actually buy them!!  It's a (in short)
cluster of 600MHz alphas with point 650MB/s interconnect.  A few years ago,
that was hot stuff, but it's not anymore.  Plenty of companies will sell
you interconnect that is that fast, and the alphas coming down the pipe are
pretty durn impressive (specFP95 of 85+).  

Dave


From chemistry-request@server.ccl.net  Tue May  9 15:59:16 2000
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From: Bob Snyder <bobs@mdli.com>
To: "'Computational Chemistry Discussion Group'" <chemistry@server.ccl.net>
Cc: Bob Snyder <bobs@mdli.com>
Subject: Use of Toxicological Information in Drug Design
Date: Tue, 9 May 2000 12:59:12 -0700 
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I would like to draw to your attention a session on the "Use of
Toxicological Information in Drug Design" at the upcoming ACS in Washington
DC (August 20-24, 2000).  The session is being organized by the Chemical
Information (CINF) division.  Below are the abstracts for the session,
beginning with the keynote address by Dr. Joseph Contrera, associate
director of the Office of Testing and Research at the FDA.

I hope to see you there.

Bob Snyder

-------------------------------------

1.  Keynote Address: "Application of toxicology databases in drug
development"
by Joseph F. Contrera and Edwin J. Matthews (FDA's Office of Testing and
Research)

In drug development, the application of combinatorial chemistry and high
through put screening of compounds has resulted in an unprecedented increase
in the number of compounds identified with potentially desirable
pharmacological properties. The selection of lead compounds is currently
hampered by limitations in the available methods for assessing toxicity.
CDER files are a unique repository of the results of clinical and
non-clinical toxicology studies. With the major advances in computer and
information technology this unique scientific resource can be more
effectively used to improve the scientific basis of regulatory decisions and
product development. A current challenge is developing means to identify
useful relationships and insights from large datasets.

Under a cooperative research and development agreement (CRADA), the FDA CDER
modified and enhanced the capability of Multicase computational toxicology
software to predict the carcinogenic potential of molecules based on
chemical structure. Such software has potential regulatory and drug
development applications that can ultimately benefit the public health.


2.  "Computational toxicology and virtual development in drug design"
by Dale E. Johnson and Grushenka H. I. Wolfgang (ddplatform LLC)

The attrition rate of lead compounds that are optimized to development
candidates and that eventually reach early clinical trials is still
alarmingly high. One key reason for the high failure rate is undesired or
unpredicted toxicity - either in animals or humans. Currently, a wide array
of predictive tools is being developed with the goal of improving lead
compound selection at the earliest stage. These new in silico approaches are
changing toxicology into a knowledge- and information-based science where
structure-toxicity-relationships are beginning to be elucidated. Predicting
potential toxicity requires knowledge of both ADME and pharmacokinetic data
across species as well as an understanding of mechanisms of action and the
chemical species that elicits the initial toxic event. Although the toxicity
"bottleneck" is formidable, virtual approaches using simulation algorithms
are expected to accelerate and increase the success of early drug
development within the next 3-5 years. 


3.  "The paradigm shift from traditional to virtual"
by Stephen K Durham (Bristol-Myers Squibb)

The intensely competitive global pharmaceutical business environment has
forced the need for the early and successful selection of viable drug
candidates, and the abandonment of the traditional development paradigm. The
enormous drug developmental costs necessitate the identification of
toxicologic liabilities of novel compounds during the initial and least
expensive phase of the discovery process. The incorporation of in silico
programs to predict toxicity, accompanied by aggressive model development,
will be fruitful avenues worth pursuit in the drug candidate evaluation
algorithm.


4.  "Application of Computational Toxicology (ComTox) and Multicase (MCASE)
Software to the FDA Mission"
by Edwin J. Matthews and Joseph F. Contrera (FDA's Office of Testing and
Research)

Under a CRADA between FDA and Multicase, Inc., new ComTox software programs
have been developed that estimate chemical-toxic responses and dosages in
animals using animal toxicology studies, and in humans using pre-market
clinical-trial data and post-market adverse-event data for pharmaceuticals.
This talk will examine two software modules that predict the potential
carcinogenicity, and the maximum-tolerated-dose (MTD), in rats and mice, and
it will elaborate on the experimental parameters that were accounted for the
program's high predictive performance and excellent coverage for
FDA-regulated substances. The parameters include: (1) large control data
sets (n>1000), (2) separate modules for each study cell (rat & mouse), (3)
the use of biological potency scales, and (4) a human expert system. The
talk will also review the current and future regulatory applications of
ComTox within the Agency. 


5.  "Data mining of toxic chemicals and database-based toxicity prediction"
by Jiansuo Wang and Luhua Lai (Peking University)

In the early stage of drug discovery, especially for computer-aided drug
design, a large number of molecules will be proposed as potential leads and
the bioactivity risk of these molecules is expected to be evaluated prior to
synthesis. The rule-based expert systems have been used for the aim, while
mining of a large amount of toxicological data can provide us with another
promise.

In term of pharmacologists/toxicologists, toxicants are the drugs that cause
vital harm. Therefore, the biochemical basis of toxic chemicals is the same
as that of drugs and there exist toxicant-receptor systems just like
drug-receptor systems. Under such a notion, we introduce some concepts and
technologies, which are developed in drug design, into toxic chemicals, and
conduct the following work.

I. We have studied the structural features of toxic chemicals from the RTECS
database associating with specific toxicity. Potential active frameworks,
groups and structure patterns for specific toxicity are obtained by
computational chemistry approaches. These structural features of toxic
chemicals will be helpful to understand activities of toxic chemicals and
useful to predict toxicity of chemicals, especially in the early stage of
drug design.

II. We take a two-step strategy to explore noncongeneric toxic chemicals
>from the database RTECS: the screening of structure patterns and the
generation of detailed relationship between structure and activity. From the
performance of overall procedure, such a stepwise scheme is demonstrated to
be feasible and effective to mine a database of toxic chemicals.

III. We develop one program as database-based toxicity predictor of
chemicals (dbToxPre). For one activity-query molecule, the program firstly
retrieves its structure-related molecule set by quick shape comparison with
the molecules in toxicological database; then carries out detailed
structure-toxicity-relation analysis to the molecule set and produce the
toxicity prediction of the query molecule. The program mainly includes four
parts: a) a fast and efficient clustering of molecules based on molecular
shape, b) field-based similarity computation of molecular structure based on
shape cluster, c) flexible CoMFA analysis of molecules based on shape
cluster, and d) a database of toxic chemicals suitable for such procedure.


6.  "In Silico Toxicology Screening of Estrogenic Compounds as Potential
Therapeutic Agents"
by William J. Welsh (University of Missouri-St. Louis)

Specific estrogen-like compounds known as Selective Estrogen Receptor
Modulators (SERMs) have attracted tremendous interest in the pharmaceutical
industry and elsewhere as potential therapeutic agents for myriad
applications in medicine. We have employed an integrated array of
ligand-based and receptor-based approaches to design a large number of
estrogen agonists and antagonists spanning several chemical classes. As part
of this drug discovery program, we have developed and applied various in
silico strategies for rapid screening of these compounds in terms of their
toxicological and environmental effects. My talk will discuss growing
concerns about the possible environmental impact of estrogenic compounds. It
will also describe our computer-based models for predicting the biological
activity and toxicological profile for the novel set of compounds under
development in this laboratory.


-------------------------------------
Robert W. Snyder, Ph.D.
Director, Chemistry Marketing
MDL Information Systems
email:   bobs@mdli.com
telephone:   510-357-2222

Never stop searching.





From chemistry-request@server.ccl.net  Wed May 10 04:14:53 2000
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Message-ID: <002701bfba57$c1341400$204f959f@farma.unimi.it.farma.unimi.it>
From: "Giulio Vistoli" <giulio.vistoli@unimi.it>
To: "CCL" <chemistry@ccl.net>
Subject: CHARMM .ENE file
Date: Wed, 10 May 2000 10:14:25 +0200
Organization: Ist. Chimica Farmaceutica
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Dear CClers,
I performed a molecular dynamic with Quanta/CHARMM using the following
parameters:

Total number of steps: 4.000.000 (4 ns)
Time step: 1 fs
Temperature: 300 K
Frame stored every 1000 step (1 ps)

Opening the resulting .ENE file, I found that energy refresh is every 300
steps instead of 1000. Analyzing the dynamics with Qunata, I'm afraid it
could read only the first 4.000 records and indeed the Quanta textport shows
the following warning message:
"Energy file read is being truncated ..."
This problem was shown using both the Quanta graphical interface and the
CHARMM script language.
It's all right ?
Thank you for your attention.


            Giulio Vistoli



From chemistry-request@server.ccl.net  Wed May 10 06:42:52 2000
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From: "Michael G. Razumov" <michraz@analyt.chem.msu.ru>
To: <CHEMISTRY@ccl.net>
Subject: MM calculation of the stacking structures
Date: Wed, 10 May 2000 14:43:45 +0300
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Dear CCLers!

Could anybody help me with a problem, concerning MM calculation of the
stacking structures?

I have (theoretically) two plane aromatic structures (Ni(II)
phtalocyaninates), one above another, bound with each other between benzene
rings by some flexible carbon chains.

The question is: will the planes come off each other if the length of these
chains is long enough? Or will they fix at some distance from each other?

For example, calculating these systems with standard molecular mechanics
with electrostatic interactions turned off, one will result in two planes at
distance about sum of van-der-Waals radii (C-C) as there is a minimum of
this function here.

_Is there any physical sense of such structure?_ Maybe, pi-pi interaction
should be also taken into account?

Probably, I need to turn on electrostatic interactions? If so, were from to
take partial atomic charges?


Thank you all for attention and for the help in advance.


----------------------------------------------------------------------------
---------
Michael G. Razumov,  Postgraduate Student of
Kurnakov Institute of General and Inorganic Chemistry
and Lomonosov Moscow State University
E-Mail: michraz@analyt.chem.msu.ru  michael@analyt.chem.msu.su
ICQ UIN: 25169010



From chemistry-request@server.ccl.net  Wed May 10 07:28:57 2000
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Date: Wed, 10 May 2000 12:28:39 +0100 (BST)
To: chemistry@ccl.net
Subject: Goldschmidt 2000 Conference - Call for Papers
X-Mailer: VM 6.75 under 20.4 "Emerald" XEmacs  Lucid

We are writing to bring to your attention the session on
COMPUTATIONAL GEOCHEMISTRY at this year's Goldschmidt Conference 
in Oxford on September 3rd to 8th.  We hope to draw together workers 
applying all types of computational methods to geochemical problems.
The meeting should be very interesting with many different sessions
and we encourage you to submit an abstract. 

The deadline for abstracts is May 15th (next Monday) and registration 
and abstract forms can be found on the Goldshmidt 2000 web site.

http://www.campublic.co.uk/science/conference/Gold2000/

We look forward to seeing you there.

Regards, Keith Refson and John Brodholt

-- 
Dr Keith Refson,        "Paradigm is a word too often used by those who would
Dept of Earth Sciences      like to have a new idea but cannot think of one." 
Parks Road,                  -- Mervyn King, Deputy Governor, Bank of England
Oxford OX1 3PR, UK        
Keith.Refson@                       Tel: 01865 272026
             earth.ox.ac.uk         Fax: 01865 272072

 

John Brodholt                    
Dept. of Geological Sciences          
University College London             
Gower Street
London WC1E 6BT

Tel : +44 (0)20-7679-2622      Fax : +44 (0)20-7388-7614
Email : j.brodholt@ucl.ac.uk          
http://slamdunk.geol.ucl.ac.uk/~brodholt


From chemistry-request@server.ccl.net  Wed May 10 09:33:35 2000
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Date: Wed, 10 May 2000 09:36:11 -0400 (EDT)
From: Sue Kong <sue@beowulf.cox.miami.edu>
To: chemistry@ccl.net
Subject: Herb Databases
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Dear all,

Does anyone know any structure and biological acitivities databases
of medicinal herbs, or where I may get more information?  

Thank you in advance,

Sue
-------------------
Sue Kong
University of Miami


From chemistry-request@server.ccl.net  Wed May 10 12:08:00 2000
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Date: Wed, 10 May 2000 18:07:38 +0200 (MDT)
From: Harald Svedung <svedung@phc.chalmers.se>
To: CHEMISTRY@ccl.net
Subject: resonance
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Hi everyone,

Does anyone have the expression for the two normal modes in a 3-atomic 
linear (without bending) molecule in terms of 3 masses and 2 
harmonic force constants?

It seems to be a textbook exrecise but I can't trust my pencilwork 
with all those masses (3).

%-)....

:-)
/Harald

Harald Svedung (Ph.Lic.)                phone:          +46-31-7722816
Department of Chemistry                 fax:            +46-31-167194
Physical Chemistry                      home phone:     +46-31-240897, +46-709223206	
Goeteborg University                    home e-mail:    harald.svedung@svedung.pp.se
SE-412 96 Goeteborg, Sweden             www.che.chalmers.se/~svedung/	


From chemistry-request@server.ccl.net  Wed May 10 12:49:46 2000
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Date: Wed, 10 May 2000 18:49:24 +0200 (MEST)
From: Ralf Flaig <flaig@chemie.fu-berlin.de>
To: chemistry@ccl.net
Subject: dipole moments of amino acids
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Dear CCLers,

I am looking for experimentally determined (by any method) values of 
amino acids. Could you point me to some relevant references?

Thanks in advance,

Ralf

--
Freie Universitaet Berlin               | Ralf Flaig     
Institut fuer Chemie                    | email: flaig@chemie.fu-berlin.de
Abteilung Kristallographie, R 111       | Tel.: +49-(0)30-838-52354 
Takustrasse 6, D-14195 Berlin, Germany  | FAX : +49-(0)30-838-53464 


From chemistry-request@server.ccl.net  Wed May 10 14:26:33 2000
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Date: Wed, 10 May 2000 20:26:33 +0200 (MEST)
From: Ralf Flaig <flaig@chemie.fu-berlin.de>
To: chemistry@ccl.net
Subject: dipole moments of amino acids
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Dear CCLers,

I just realized that my previous mail was a bit unclear. Sorry for
posting my question again.

I am looking for experimentally determined (by any method) values of
dipole moments of amino acids in their neutral or zwitterionic form.
Could you point me to some relevant references?

Thanks in advance,

Ralf

--
Freie Universitaet Berlin               | Ralf Flaig     
Institut fuer Chemie                    | email: flaig@chemie.fu-berlin.de
Abteilung Kristallographie, R 111       | Tel.: +49-(0)30-838-52354 
Takustrasse 6, D-14195 Berlin, Germany  | FAX : +49-(0)30-838-53464 


From chemistry-request@server.ccl.net  Wed May 10 17:42:55 2000
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Date: Wed, 10 May 2000 23:42:53 +0200
From: "Dr. Peter Burger" <chburger@aci.unizh.ch>
To: CHEMISTRY@ccl.net
Subject: Robin Day Classifications
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Dear CClers,

I know this is once again off topic..
but maybe someone just has the Robin Day
classifications based on their comproportionation
constants (by electrochemistry) just available.
Either K or delta_Ep values were helpful.
Many thanks in advance.

Peter
-------------------------------------
Peter Burger
University of Zuerich
chburger@aci.unizh.ch



From chemistry-request@server.ccl.net  Wed May 10 19:14:41 2000
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Date: Wed, 10 May 2000 18:13:11 -0500 (CDT)
From: "P.H.Lakshminarasimhan" <lpranat@mailhost.tcs.tulane.edu>
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To: chemistry@ccl.net
Subject: Zeolite Model
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Hello everyone,
I was wondering if anyone had a model of zeolite Y or X(faujasite) either
in .hin or .ent format. I would reallr appreciate any response in this
regard.
Thanks in advance
Haran


From chemistry-request@server.ccl.net  Wed May 10 22:53:44 2000
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Date: Thu, 11 May 2000 10:59:19 +0800 (CST)
From: Fenglou Mao <mao@linux2.ipc.pku.edu.cn>
To: "CHEMISTRY@www.ccl.net" <CHEMISTRY@server.ccl.net>
Subject: Superpose algrithm?
Message-ID: <Pine.LNX.4.10.10005111058270.17926-100000@linux2.ipc.pku.edu.cn>
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Hi, all,
    Who introduce some superpose algrithm or some
reference?
    Thanks a lot.

Sincerely Yours,

FengLou Mao
*******************************
ADD:Mr. FengLou Mao
    Institute of Physical Chemistry
    Peking University
    BeiJing
    P.R.China
Tel:86-10-62756833
Fax:86-10-62751725


