postdoc Advanced Visualization & Molecular Docking

[Sylvain Petitjean]

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LORIA/INRIA and LCTN laboratories
Nancy, France

Post-Doctoral Position Available

We have an opening for a post-doctoral fellow for up to 2 years, commencing 
september/october 2002 or later, to work on:

Enhancing Molecular Docking Through High-Performance Computing and
Advanced Visualization

Molecular docking is the natural process by which molecules recognize and
interact with one another.  From a computational standpoint, it also refers
to the prediction of the structures of ligand-receptor complexes from the
conformations of unbound ligand and unbound receptor.  Molecular docking is
at the center of such practical applications as protein engineering and
drug design.  It has already helped to design new ligands for anti-AIDS and
anti-cancer agents and for the treatment of diabetes.

Structure-based molecular docking programs are based on the assumption that
ligands which form favorable interactions with the receptor must have high
binding affinity.  They rely on the number-crunching capabilities of
computers to generate and evaluate large numbers of possible bindings. 
Computers however do not have the experience of human beings and molecular
docking methods severely limit the biochemists' ability to analyze the
bindings computed and exploit their intuition and expertise to generate
sound and reliable solutions.  Also, most approaches to molecular docking
do not take advantage of the visualization capabilities offered by modern
workstations.

Major challenges in this field are (1) predicting how molecules will dock
with one another and (2) identifying the factors that determine the
specificity of interaction.  To make significant advances, it is necessary
to develop novel methods to facilitate the docking techniques by enhancing
our ability to understand and analyze docking interactions and to develop
hypotheses about which molecules are most likely to interact favorably. 
These factors can be incorporated into molecular docking by including
advanced visualization and haptic (sense of touch) feedback in the process.

The main goal of this project is to develop an immersive, interactive and
easy-to-use modelling environment to enhance molecular docking.  The
candidate will have at its disposal the state-of-the-art SGI
high-performance computing technologies available at LORIA, notably the
Reality Center immersive visualization facility and the Onyx 3800 
shared-memory system platform.

In particular, the postdoctoral candidate is expected:
- To integrate existing molecular docking programs with the LORIA 
  collaborative computing environment.
- To implement a haptic interface to facilitate interaction with molecular 
  models, through a high-fidelity, 3D force-feedback device.
- To combine visualization and haptic feedback to allow interactive docking 
  simulations in the Reality Center.
- To develop a multimodal user interface to facilitate the work of 
  molecular scientists.

The successful candidate will have a solid background in SGI graphics
software and architecture.  He is also expected to have a working knowledge
of programming and scripting languages such as Java, Perl and TCL/TK.
Candidates having experience in parallel computing and/or grid computing
will be given priority.

Salary will be approximately 21400 euros per annum.  There are no
restrictions on the nationality of the applicant.

For more information on this position as well as indication of interest,
please contact either

Bernard Maigret (Bernard.Maigret at lctn.uhp-nancy.fr)
http://www.lctn.uhp-nancy.fr

or

Sylvain Petitjean (Sylvain.Petitjean at loria.fr)
http://www.loria.fr




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