Tuesday, October 29, 2013

[DMANET] PhD thesis on computational geometry and structural bioinformatics

Contact: Therese Malliavin <terez@pasteur.fr>

Title: Computational geometry for the determination of biomolecular structures

During the last decades, structural biology allowed to incredibly
improve the information on the biological objects, from single
biomolecules to molecular assemblies, and to get a better description
of the physics underlying the interactions between molecules.
Somehow, structural biology can be considered as the description
of the geometric properties of biomolecules, as biomolecular
structures are determined from the measurements of angles and
distances between molecule atoms. These parameter values can
be determined by: Nuclear Magnetic Resonance (NMR), fluorescence/FRET,
mass spectrometry coupled to cross-linking or analysis of protein
sequence alignment. Up to now, one of the most used method to
optimize the protein conformation given these geometric restraints,
was based on the repeated use of simulated annealing (SA) algorithm,
followed by extensive statistics. As the SA algorithm does not
provide a guarantee of global minimality of the function, and
is quite sensitive to the sparsity and to the lack of redundancy
in the distance restraints, we propose in this PhD thesis to explore the
efficiency of another class of methods, derived from operations research
and computational geometry, where a branch-and-pruning algorithm permits
in principle the full exploration of the whole solution space. This
algorithm already gave promising results on small examples of biomolecules,
and the purpose of the project would be to extend them to real-life
systems including: protein structures determination from NMR
distance restraints, homology models or positioning of protein
domains within molecular assemblies using cross-linking restraints.
The PhD thesis will be realized in the frame of a collaboration between the
UnitÈ de Bioinformatique Structurale (CNRS/Institut Pasteur, France) and
the Department of Applied Mathematics (University of Campinas, Brazil).

Required skills
Knowledge of the basic features of the protein structure
Knowledge of algorithmics
Knowledge of at least one programming language among: C++, python

Will to work in an inter-disciplinary team with interactions
with biologists and applied mathematicians

Required level:
Master in bioinformatics including courses on structural bioinformatics,
computer science or applied mathematics

Working language: english, french

Contact: Therese Malliavin
Unite de Bioinformatique Structurale
Institut Pasteur and CNRS, Paris

Doctoral school: IViV, the student should be able to register at the University
before starting the PhD.
Salary paid by Institut Pasteur
Salary: 1450Euros/month, but the income taxes have to be paid on it
(other charges are already removed).
Work permit required from foreigners outside of the Schlengen space.
Application deadline: December, 1st, 2013
The following documents are required from the applicant:
motivation letter, CV, details of undergraduate and master studies
with marks, master dissertation or any paper the student might have
already written.
Funding is only for three years, starting as soon as the application if

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