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Date: Tue Sep 25 09:29:50 2018
Subject: 18.09.25 Paris Pasteur University International Doctoral Program. Automatic Building of Protein Atomic Models from Cryo-EM Maps using evolutionary coupling data (EMEC: Electron Microscopy and Evolutionary Coupling)
Automatic Building of Protein Atomic Models from Cryo-EM Maps using
evolutionary coupling data (EMEC: Electron Microscopy and Evolutionary
Coupling)

The Institut Pasteur has just inaugurated the installation of a new electron
microscope equipped with extraordinary capabilities: the new Titan Krios.
Cryo-electron microscopy (Cryo-EM) has emerged as a powerful method to obtain
electron density maps of protein assemblies. Albeit the incredible resolution
of the data obtained by this new generation of microscopes, reconstruction of
atomic models from near atomic resolution (3-5 ) cryo-EM maps is still
challenging. Several tools developed for X-ray crystallography are widely used
to interpret high resolution EM maps (around 3 ), but poorly resolved
side-chain densities hamper sequence attribution by automatic procedures at
lower resolution.  Furthermore, segmentation of EM maps into subunits remains a
difficult problem when no structures of these subunits exist, or when
conformational changes occur between the isolated and complexed form of the
subunits. The aim of the project is to first develop a graph-based method to
thread most of the C- trace of the protein backbone into the EM map. The EM
density is described as a weighted graph such as the resulting minimum spanning
tree encompasses the high density region of the map. A pruning algorithm is
then applied to clean the tree and find the most probable positions of the C-
atoms, using sidechain density when available, in the form of C- trace
fragments. Then the challenge of the approach is to complement the experimental
EM maps with contact predictions from sequence co-evolutionary information to:
(i) segment correctly the EM maps into individual subunits and thus identify
the regions of the different protein partners and (ii) register the protein
sequence onto the initial thread found using the graph based approach described
previously. Therefore, once the sequence registered, the full-atom protein
structure could be modelled onto the density. Once the method developed and
implemented, it would be benchmarked onto several Cryo-EM data and applied onto
real structural studies of new protein complexes.
The Institut Pasteur in Paris organizes a doctoral program in collaboration
with the universities Paris-Descartes, Paris-Diderot, Pierre and Marie Curie,
and Paris-Sud, for students holding a master degree or the equivalent in
science, medicine and related fields delivered by a university outside of
France.

In 2009, the Institut Pasteur, the world leading biomedical research institute
founded by Louis Pasteur in 1887, inaugurated the Pasteur Paris-University
(PPU) international doctoral program in collaboration with several major
Parisian science universities for students holding a Master degree (or
equivalent) from a university outside of France and who have not worked or
resided in France for more than 12 months in the 3 years prior to their
recruitment.

The 2018-2019 call for enrollment of students in October 2019 is open until
November 2nd, 2018.

Please go to the dedicated platform: https://ppu.pasteur.fr where you can find
the project described (EMEC project) and to submit your application.

Deadline for contacting host laboratories: November 2, 2018
Deadline for submitting the application with the host laboratory: November 13, 2018
Interview week: January 29 / February 1, 2019

Contact: guillaume.bouvier^^pasteur.fr
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