Subject: 03.06.27 2nd Conf on MODELING OF PROTEIN INTERACTIONS IN GENOMES

From: Jan Labanowski <[email-masked]>
Date: Sun, 6 Apr 2003 23:14:57 -0400 (EDT)

---------- Forwarded message ----------
Date: Sun, 06 Apr 2003 12:02:54 -0400
From: Ilya Vakser <[email-masked]>
To: [email-masked]
Subject: 2nd Conference on MODELING OF PROTEIN INTERACTIONS IN GENOMES

Hi,
We would like to post the conference announcement (see below) on your
web site, as well as distribute it to the CCL subscribers.
Thank you!
Ilya Vakser

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2nd Conference on MODELING OF PROTEIN INTERACTIONS IN GENOMES
June 27-30, 2003, Stony Brook, NY 

*** CALL FOR PAPERS ***

The conference focuses on computational procedures for reconstruction
and study of the network of connections between proteins in genomes.

The sponsors are: National Science Foundation and State University of
New York at Stony Brook.

The conference is organized by Ilya Vakser (SUNY Stony Brook) and Sandor
Vajda (Boston University).

PROGRAM topics:

PROTEIN-PROTEIN DOCKING
(structure prediction and binding simulation)
ENERGETICS AND PROTEIN STRUCTURE-FUNCTION RELATIONSHIPS
(energy landscapes, stability of complexes, functional assignment of
protein structures, binding site prediction)
MACROMOLECULAR ASSEMBLIES AND MEMBRANE PROTEINS
IDENTIFICATION OF INTERACTIONS AND PATHWAYS
DISCUSSION: New directions at CAPRI and further developments

Tentative (incomplete) list of speakers:

Ruben Abagyan, Scripps Institute
David Baker, University of Washington
Carlos Camacho, Boston University
Adam Godzik, Burnham Institute 
Barry Honig, Columbia University 
Joel Janin, Centre National de la Recherche Scientifique 
Robert Jernigan, Iowa State University
Olivier Lichtarge, Baylor College of Medicine
Garland Marshall, Washington University
Sergei Maslov, Brookhaven National Laboratory
Andrew McCammon, University of California San Diego 
John Moult, CARB, University of Maryland
Ruth Nussinov, National Cancer Institute 
Arthur Olson, Scripps Institute 
Jeffrey Skolnick, University at Buffalo 
Michael Sternberg, Imperial College London
Lynn Ten Eyck, San Diego Supercomputer Center
Andrei Tovchigrechko, SUNY Stony Brook
Harel Weinstein, Weill Medical College of Cornell University
Zhiping Weng, Boston University
Shoshana Wodak, University Libre de Bruxelles 
Peter Wolynes, University of California San Diego
Willy Wriggers, University of Texas Health Science Center

(additional speakers will be selected based on participants
applications) 

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

PARTICIPATION

The number of participants is limited to 100. In selecting participants,
the preference will be given to those who would have a presentation on
the subject of the conference. If you would like to attend the
conference, please submit a request as soon as possible, by e-mail only,
to Ilya Vakser ([email-masked]) or Sandor Vajda
([email-masked]). Include a brief (a few sentences) description of
your research, your full affiliation, position (faculty, postdoc,
student, etc.), address (email and regular), and the day-time phone
number. If you would like to give a talk or present a poster, please
include a half-page abstract. We will start contacting prospective
participants after April 27 to let them know whether their application
is accepted. If your application is accepted, we will communicate with
you regarding the details of registration, accommodation, and travel.  

The early registration fee for the participants of the conference will
be $250 ($150 for postdocs and students). Limited funds are available to
support the participation of postdocs and students. The postdocs and
students, who wish to be considered for the financial assistance, should
indicate this in their application. The assistance will be provided in
the form of reimbursement of travel expenses, after the conference.

The details of the conference will be posted at the conference web site,
http://reco3.ams.stonybrook.edu/conference2003 , which will be regularly
updated.

---

From: "Duc Nguyen" <[email-masked]>
Date: Mon, 7 Apr 2003 12:25:24 -0400

Hi all,

Normally, how would you estimate the intrinsic Arrhenius activation energy
of a reaction pathway. Would you use:

1/ the potential energy of the transition state

2/ the difference in potential energy between the transition state and the
reactants: (classical energy barrier)

3/ the difference in zero-point energy between the transition state and the
reactants: (quantum energy barrier)

4/ the difference in heat of formation between the transition state and the
reactants

Laidler (Chemical Kinetics, 1987) showed the differents between the last 3
and derived an equation to calculate the instrinsic Arrhenius activation
energy from the difference in heat of formation between the transition state
and the reactants as: Ea = deltaHf_transitionstate - deltaHf_reactants + RT
(for reaction in solution and unimolecular gas phase reactions).

How does MOPAC or other quantum mechanisc package calculate the potential
energy and zero-point energy of a compound? How normally are they different?
Does it vary from compounds to compounds?

Thank you very much in advance,
Regards,
Duc