Postdoc in bioinformatics

Dr. Ioannis Emiris Ioannis.Emiris at
Tue Apr 16 13:07:19 PDT 2002

Distance Geometry and High-throughput Structural Genomics by NMR

English announcement:

Annonce française:

Within the framework of a Bioinformatics Project among CNRS,

Keywords: Bioinformatics, Structural Biology, Data Processing,
Distance Geometry, Conformational Search 

Duration: one year 

Laboratoire de Biochimie Theorique (IBPC, Paris): 8 months
Laboratoire GALAAD (INRIA Sophia-Antipolis): 4 months 

Financial support: ~1780 Euro /month net ie. ~2200 Euro /month gross
(INRIA postdoctoral fellowship) 

Availability of the support: April 2002 

Profile: Scientist, having a PhD in 
- structural biology, bioinformatics or molecular modelling, 
- or in algorithm design or applied mathematics. 
The postdoc fellow will spend some time in each of the two labs
indicated above, namely 8 and 4 months respectively. A practical
ability in programming (C, C++, Fortran, perl, cgi scripts) will
be appreciated. A wish to enlarge his scientific horizons and an
ability to communicate with scientists from other fields is essential. 

Structural biology has significantly evolved, during the last years,
following the massive increase of information on proteins, coming
from genomics projects. A new approach of structural problems
appeared, namely structural genomics, in which the structure of a
large number of proteins has to be determined and moreover, as much
as this is possible, in an automatic way. The methods for structure
determination are those of classical structural biology: NMR and
X-ray crystallography. But they have to be modified in order to increase
throughput. One major problem in applying NMR to structural
genomics projects is the long step of spectral assignment by hand,
during which the signal produced on a protein sample by NMR
spectrometers has to be analyzed in order to determine the structural
parameters which will be used for structure determination. 

The project presented here consists of developing methods of fast
determination of protein structure from unassigned NMR spectra, and
in making these methods available to the scientific community as
Internet tools. These tools will complete an existing server
predicting the amino-acid type from the chemical shifts of their
hydrogens and a database of raw NMR spectra.

The project will use the methods already developed by the two
partner laboratories: 
- Geometry, Algebra and Algorithms for the GALAAD team (Ioannis Z.
Emiris and Bernard Mourrain, INRIA Sophia-Antipolis). Related
publication: Emiris, I.Z., and Mourrain, B. (1999) "Computer
algebra methods for studying and computing molecular conformations",
- Analysis and automatic assignment of NMR spectra for the group
in the Laboratoire de Biochimie Théorique (Thérèse Malliavin, IBPC,
Paris), in relation with the Centre de Biochimie Structurale (CBS:
Marc-André Delsuc and Jean-Luc Pons). Related publications: Pons,
J.L., and Delsuc, M.A. (1999) "RESCUE: an artificial neural network
tool for the NMR spectral assignment of proteins", J. Biomol. NMR 15,
15-26. Malliavin, T.E., Barthe P., and Delsuc, M.A. (2001) "FIRE:
predicting the spatial proximity of protein residues from a 3D
HSQC-NOESY", Theor. Chem. Accts 106, 91-97. 

The bioinformatics tools developed in the frame of this project
will be tested on real-life data recorded on Lipid Transfer
proteins. The protein samples will be over-expressed in the
Laboratoire de Biochimie et Biologie Moléculaire des Ceréales
(INRA - Montpellier). Related publication: de Lamotte, F., Boze, H.,
Blanchard, C., Klein, C., Moulin, G., Gautier, M.F., and Delsuc M.A.
(2001) "NMR monitoring of accumulation and folding of 15N-labeled
protein overexpressed in Pichia pastoris", Protein Expr. Purif. 22,

Applications should include a CV and the candidate's publications,
if any. For submitting applications (preferably
electronically) or further inquiries, please contact: 

                   Thérèse MALLIAVIN 
                   Charge de Recherches au CNRS 
                   Laboratoire de Biochimie Theorique 
                   Institut de Biologie Physico-Chimique 
                   13, rue P. et M. Curie 
                   F-75005 Paris 
                   Mail: Therese.Malliavin at 
                   Tel: (33) +1 58 41 51 68 
                   Fax: (33) +1 58 41 50 26

Ioannis EMIRIS, PhD     Tenured researcher
INRIA Sophia-Antipolis 	B.P. 93, 06902 France
tel +33-4-9238-7651     Ioannis.Emiris at	 
fax +33-4-9238-7978

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