From owner-molmodel@hgmp.mrc.ac.uk  Tue Sep  5 11:26:18 2000
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From: A.van.Ooyen@nih.knaw.nl (Arjen van Ooyen)
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Subject: Competition for Neurotrophins
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New Paper:

Development of Nerve Connections under the Control
of Neurotrophic Factors: Parallels with
Consumer-Resource Systems in Population Biology.

Arjen van Ooyen & David J. Willshaw, 
J. Theor. Biol. (2000) 206: 195-210.

Download in gzipped PostScript format 
or PDF format from:

http://www.anc.ed.ac.uk/~arjen/competition.html

or request reprint:

A.van.Ooyen@nih.knaw.nl 


Abstract
--------

We show that a recently formulated model of axonal competition can be
rewritten as a general consumer-resource system. 
This allows neurobiological phenomena to be interpreted in population
biological terms and, conversely, results from population biology 
(where competition is better understood) to be applied to neurobiology. 
Using findings from population biology, we study two extensions of our
axonal competition model. In the first extension, the spatial dimension 
of the target is explicitly taken into account. We show that distance
between axons on their target mitigates competition and permits the
coexistence of axons. The model can account for the fact that, in many
types of neurons, a positive 
correlation exists between the size of the dendritic tree and the number 
of innervating axons surviving into adulthood. In the second extension,
axons are allowed to respond to more than one neurotrophic factor. We
show that this permits competitive exclusion within one type of 
axons, while at the same time there is coexistence with a different 
type of axons innervating the same target. The model offers an
explanation 
for the innervation pattern found on cerebellar Purkinje cells, where 
climbing fibres compete with each other until only a single one remains,
which
coexists with parallel fibre input to the same Purkinje cell. 



-- 
Arjen van Ooyen, Netherlands Institute for Brain Research,
Meibergdreef 33, 1105 AZ Amsterdam, The Netherlands.
email: A.van.Ooyen@nih.knaw.nl 
website: http://www.anc.ed.ac.uk/~arjen
phone: +31.20.5665483  fax: +31.20.6961006


---




From owner-molmodel@hgmp.mrc.ac.uk  Wed Sep  6 18:06:39 2000
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From: j1000@algeriamail.com
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Subject: EARN 2-5K PER WEEK!
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From owner-molmodel@hgmp.mrc.ac.uk  Wed Sep  6 22:07:19 2000
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Message-ID: <39B6B203.7DC40ECB@ks.uiuc.edu>
From: Jim Phillips <jim@ks.uiuc.edu>
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Subject: NAMD 2.2b1 Release Announcement
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+--------------------------------------------------------------------+
|                                                                    |
|                  NAMD 2.2b1 Release Announcement                   |
|                                                                    |
+--------------------------------------------------------------------+

                                                   September 5, 2000

The Theoretical Biophysics Group at the University of Illinois is
proud to announce the public release of a new version of NAMD, a
parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.2b1 has several advantages over NAMD 2.1:

- Parallelized particle mesh Ewald FFT and reciprocal space sum
  with demonstrated scaling to 128 processors for large systems.

- Release binaries contain FFTW (under special license) for
  better serial performance when using particle mesh Ewald.

- Much faster minimizer based on conjugate gradient method, also
  more stable when dealing with very bad initial contacts.

- Improved load balancer with demonstrated scaling to over
  1024 processors for large cutoff systems.

This is a beta release!  Please be on the lookout for bugs, memory
leaks, and instabilities of all kinds and report them immediately.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

The Theoretical Biophysics group encourages NAMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.  Questions or comments
may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!




From owner-molmodel@hgmp.mrc.ac.uk  Thu Sep  7 18:39:58 2000
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From: helma@informatik.uni-freiburg.de (Christoph Helma)
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Subject: ANNOUNCEMENT: The Predictive Toxicology Challenge 2000-2001
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***************************** ANNOUNCEMENT ****************************** 
*                                                                       *
*             THE PREDICTIVE TOXICOLOGY CHALLENGE 2000-2001             *
*                                                                       *
*************************************************************************

We initiated the Predictive Toxicology Challenge (PTC) to stimulate the
development of advanced SAR techniques for predictive toxicology models
with nocongeneric compounds. The goal of this competition is to predict
the rodent carcinogenicity of new compounds based on the experimental
results of the US National Toxicology Program (NTP). The PTC will last
from 2000 to 2001 and consist of four stages.

In Phase I chemical structures and carcinogenicity evaluations from
the NTP will be provided by the organizers. Participants can submit new
chemical and structural descriptors for these molecules before March 01,
2001. These submissions will be used by the model-developers in Phase II.

In Phase II predictive toxicology models based on descriptors from Phase
I may be submitted until June 01, 2001. Each submission must include
an estimation of the model accuracy according to the rules given on
the website and a translation of the model, which is understandable
by toxicologists.

In Phase III the submitted models will be evaluated on quantitative
(performance) and qualitative (toxicological relevance) scales. From all
submissions we will select a subset of "optimal" models. From these we
will (a) identify models that are particular relevant to toxicology
and (b) descriptors that were particular useful for predicting
carcinogenicity.

Finally, the results of the Predictive Toxicology Challenge 2000-2001
will be presented at a workshop of the PKDD/ECML conferences in September
2001 in Freiburg.

Detailed information about the Predictive Toxicology Challenge can be
obtained from the website http://www.informatik.uni-freiburg.de/~ml/ptc/.

PS: This message was crossposted to several newsgroups and mailinglists to
reach a broad audience. Please accept my apologies if you receive multiple 
copies of this message. 

--
Christoph Helma
Machine Learning Lab
Institute for Computer Science 
Albert-Ludwigs-Universität Freiburg  
Am Flughafen 17  
D-79110 Freiburg/Br.  
Germany 
T: +49-761-203-8013, F: +49-761-203-8007 
helma@informatik.uni-freiburg.de
http://helma.informatik.uni-freiburg.de/


---




From owner-molmodel@hgmp.mrc.ac.uk  Mon Sep 11 14:09:20 2000
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From: Aaron Turner <agt3@york.ac.uk>
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Subject: Looking for reference systems
Date: 11 Sep 2000 13:09:15 GMT
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I am working on a 3d molecular matching system using neural relaxation
(see my papers in ICANN '99, KES 2000, etc.). I am looking for some more
reference systems to compare my system against, but I am having problems
finding existing implementations of 3d molecular matching systems for
small molecules that are shareware of freeware. Can anyone point me to
any good sources? I have done various web searches, but tracking anything
down is rather difficult on the web these days.

I have a few implementations by a colleague of some other algorithms (EM,
Hodgkin scores, etc), but they are a little old now. Basically I am
looking for source code so I can control compilation to ensure I am using
the same levels of optimisation, etc, as my system to ensure a fair
comparasion. The problem I am aiming to solve is that of matching small
molecules against elements of a database of several tens of thousands of
target molecules.

Any hints/help would be greatly appreciated.

Aaron Turner,
Experimental Officer,
Advanced Compuer Architecture Group,
Department of Computer Science,
University of York.




From owner-molmodel@hgmp.mrc.ac.uk  Tue Sep 12 05:11:12 2000
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---




From owner-molmodel@hgmp.mrc.ac.uk  Tue Sep 19 16:50:35 2000
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+--------------------------------------------------------------------+
|                                                                    |
|                  NAMD 2.2b2 Release Announcement                   |
|                                                                    |
+--------------------------------------------------------------------+

                                                   September 15, 2000

The Theoretical Biophysics Group at the University of Illinois is
proud to announce the public release of a new version of NAMD, a
parallel, object-oriented molecular dynamics code designed for
high-performance simulation of large biomolecular systems.  NAMD is
distributed free of charge and includes source code.  NAMD development
is supported by the NIH National Center for Research Resources.

NAMD 2.2b2 has several advantages over NAMD 2.1:

- New ports to the IBM RS/6000 SP and Windows NT.

- Parallelized particle mesh Ewald FFT and reciprocal space sum
  with demonstrated scaling to 128 processors for large systems.

- Release binaries contain FFTW (under special license) for
  better serial performance when using particle mesh Ewald.

- Much faster minimizer based on conjugate gradient method, also
  more stable when dealing with very bad initial contacts.

- Improved load balancer with demonstrated scaling to over
  1024 processors for large cutoff systems.

This is a beta release!  Please be on the lookout for bugs, memory
leaks, and instabilities of all kinds and report them immediately.

NAMD is available from http://www.ks.uiuc.edu/Research/namd/.

The Theoretical Biophysics group encourages NAMD users to be closely
involved in the development process through reporting bugs, contributing
fixes, periodical surveys and via other means.  Questions or comments
may be directed to namd@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!




From owner-molmodel@hgmp.mrc.ac.uk  Tue Sep 19 17:20:21 2000
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esto es una prueba






From owner-molmodel@hgmp.mrc.ac.uk  Wed Sep 20 23:43:42 2000
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From: princess28677@yahoo.com ("princess28677@yahoo.com")
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Subject: phone rates
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---




From owner-molmodel@hgmp.mrc.ac.uk  Thu Sep 21 17:21:58 2000
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From: kungl@hermes.kfunigraz.ac.at ("Kungl, Andreas")
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Subject: 4th International Conference on Molecular Structural Biology (ICM
	SB2001)
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         FIRST ANNOUNCEMENT

FOURTH INTERNATIONAL CONFERENCE
ON MOLECULAR STRUCTURAL BIOLOGY

                  ICMSB2001

      5th-9th SEPTEMBER 2001
             VIENNA, AUSTRIA

(please visit our homepage at
http://pharmchem.kfunigraz.ac.at/icmsb/
for preregistration for the ICMSB2001=20
and the latest update of the programme)

We are pleased to announce the 4th International=20
Conferenceon Moecular Structural Biology (ICMSB2001)=20
which aims to bring together scientists from the=20
fields of X-ray crystallography, NMR spectroscopy,=20
molecular biology, structure prediction, computer=20
modeling and structural genomics. Vienna is again=20
the location for the ICMSB, being one of central=20
Europe=B4s most beautiful cities, with its stunning=20
architecture and numerous parks. The city also has=20
an international airport and an excellent public=20
transport system.=20

Preliminary Scientific Programme

Honorary Speaker: J=FCrgen Drews=20
(Int. Biomed. Management Partners)

Structural Molecular Biology:
Ad Bax (NIH)
Kiyoshi Nagai (MRC Cambridge)
Brian Sykes (University of Alberta)

Folding and Function:
Brian Matthews (University of Oregon)
Eugene Shakhnovich (Harvard University)
Manfred Sippl (University of Salzburg)

Macromolecular Structures:
Johann Deisenhofer (Texas University)
Dino Moras (Universit=E9 Louis Pasteur)=20
John Walker (MRC Cambridge)
Ian Wilson (Scripps Institute)=20

Structure-Based Design:
Torben Borchert (Novo Nordisk)
Ursula Egner (Schering)=20
J=F6rg Kallen (Novartis)
Kal Ramnarayan (Structural Bioinformatics Inc.)

Structural Genomics:
Barry Honig (Columbia University)
Tom Peat (Structural GenomiX Inc.)
Andrej Sali (Rockefeller University)=20

Participation Fees:=20

Early Fee (before 31st July 2001)

Regular................5.000,- ATS
G=D6CH Member.....4.000,- ATS
Student................2.500,- ATS
Accompanying person......600,- ATS

Late Fee  (after 31st July 2001)

Regular................5.500,- ATS  =20
G=D6CH Member.....4.500,- ATS    =20
Student................3.000,- ATS=20
Accompanying person......600,- ATS	=20

The fee for regular participants, G=D6CH members,=20
and students, includes the full scientific=20
programme, the Conference Proceedings (which=20
will be published in book form with an ISBN number),=20
lunch from Thursday to Saturday, coffee breaks,=20
and the entertainment programme. Accompanying=20
persons attend only the entertainment programme.=20
=20
Deadlines:=20
=20
Abstract Submission......20th July 2001
Early Registration...........31st July 2001

Conference Secretariat: =09

Dr. Andreas Kungl=20
Austrian Chemical Society (G=D6CH),=20
Biochemistry Subgroup
c/o Institute of Pharmaceutical Chemistry,=20
University of Graz, Universit=E4tsplatz 1,=20
A-8010 Graz
Tel.: +43 316 380 5373
Fax: +43 316 382541
E-Mail: andreas.kungl@kfunigraz.ac.at



---




From owner-molmodel@hgmp.mrc.ac.uk  Mon Sep 25 17:54:52 2000
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From: delgadoi@pilot.msu.edu (Ivan Delgado)
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Subject: chemistry question
Date: 25 Sep 2000 17:54:47 +0100
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Dear All,

    Anybody has an idea what the chemistry of following reaction would be?:

The glycosylation of an Arginine amino acid with the glucose from
UDP-glucose.=20

    I have a protein that can bind UDP-glucose and glycosylate itself at an
Arginine and I am trying to figure out how this can take place.
   =20
    Any ideas or a source of information regarding this question is
appreciated.

    Sincerely,
    Ivan


Ivan J. Delgado Orlic
Graduate Student=20
MSU-DOE-Plant Research Laboratory
Genetics Department
Michigan State University
178 Wilson Rd.=20
122 Plant Biology Building
East Lansing, MI=A0 48824-1312
Email: delgadoi@pilot.msu.edu
URL: http://www.msu.edu/~delgadoi/
Phone: 517-353-3519
FAX: 517-353-9168=20

Francis Crick goes to heaven: "'God,' said the angel, 'This is Dr. Crick;
Dr. Crick, this is God.' 'I am so pleased to meet you,' says Francis. 'I
must ask you this question. How do imaginal disks work?'. "'Well,' comes th=
e
reply, 'We took a little bit of this stuff and we added some things to it
and... actually, we don't know, but I can tell you that we've been building
flies up here for 200 million years and we have had no complaints.'"
-Dr. Sydney Brenner, NYT March 7, 2000



---




From owner-molmodel@hgmp.mrc.ac.uk  Fri Sep 29 19:20:07 2000
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From: "y.k.y" <y.k.y@lycos.com>
X-Newsgroups: bionet.molec-model
Subject: activation complex, free energy calculation
Date: Sat, 30 Sep 2000 02:23:16 +0800
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Hi

For some simple reactions such as
    N2 + H2 -> N2H2
    N2H2 + H2 -> N2H4
etc,  I want to find the free energies of the activation
complexes, and other data that are useful in designing
catalysts for them.  Is it possible to do this on a
single PC and with free software?  Thanks alot!!

yan king yin
y.k.y@lycos.com






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