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We are seeking candidates for a ~2 years post-doc in combinatorial
optimization applied to computational protein design problems in our
team inside the "Applied mathematics and Computer Science" lab at INRA,
Toulouse, France (mia.toulouse.inra.fr). The project is done in
collaboration with structural biologists from the "Biosystems and
Process Engineering Laboratory" (LISBP-INSA) in Toulouse.
The candidate will contribute to the improved exact resolution of
Computational Protein Design problems especially when part of the
flexibility of the protein being optimized is taken into account. Recent
applications of AI based (constraint programming) approaches developped
in our team to rigid/discrete Computational Protein Design problems have
shown very important speedups compared to usual exact approaches for
this problem, either for finding optimal solutions (Global Minimum
Energy Conformations) or enumerating "close to optimal" solutions (see
[1]). Based on these results, the candidate will explore the possibility
of dealing either with situations where some of the protein flexibility
is explicitely represented or with alternate criteria such as affinity.
It is expected that this will also bring back generic algorithmic
improvements in the area of (weighted) constraint programming, targeted
at Computer Science/AI journals. The work will be carried out in close
interaction with computer scientists in the lab and with structural
biologists at INSA and may include a visit to a US lab developping CPD
optimization tools already accouting for protein flexibility.
We are looking for a highly motivated computer scientist with either a
research background in combinatorial optimization using AI (SAT,
Constraint programming...) or Operations research (ILP, QP) methods or a
background in Structural biology with a strong emphasis on computational
techniques. Excellent programming skills are expected. Research will be
carried out in close collaboration with other laboratories. Applicants
should enjoy teamwork and have good communication skills. A good English
level is mandatory, notions of French would be a big plus. For computer
scientists, experience in computational biology and more specifically
structural biology applications is another great plus but is not mandatory.
The post-doc could start as early as the beginning of year 2014, under
an Agreenskill contract offering a typical 40% salary bonus compared to
regular post-docs in France (which is around 3,500 euros/month gross
salary). Agreenskill has specific requirement for applicants. Among
others (see
http://www.agreenskills.eu/agreenskills-cms/Applications/Eligibility-Requirements),
it is required that the applicant has spent less than 1 year in France
within the last 3 years prior to recruitment.
Applications, including a CV, a cover letter and contact information of
at least two references, should be sent by email to Thomas Schiex
([email protected]) with subject: "CPD postdoc application".
[1] *A New Framework for Computational Protein Design through Cost
Function Network Optimization*
<http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btt374?ijkey=6s5WwvLNn88x2ZB&keytype=ref>/
S. Traoré, D. Allouche, S. de Givry, G. Katsirelos, T. Schiex, S.
Barbe/, Bioinformatics, 2013.
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