Date : 13/03/2012

Laboratory
Laboratoire de Biochimie Théorique
UPR 9080, CNRS
13 rue Pierre et Marie Curie
75005 Paris
Website
Main discipline : Bioinformatics
Lab director : Philippe Derremeaux

PhD Supervisor
Antoine Taly
email : Cet e-mail est protégé contre les robots collecteurs de mails, votre navigateur doit accepter le Javascript pour le voir
phone: +33 1 58 41 51 66

Subjects
1.: protein conformational changes
2.: low energy path
3.: scientific discovery game

Tools and Methodologies
1.: normal mode analysis
2.: network analysis


This project has applied for a european funding (Marie Curie FP7 ITN IDP 2012)
within the "Wiser Games" Innovative Doctoral Program of the FdV School.

* Eligible candidates under ITN IDP regulations :

- Early Stage Researchers must be (at the time of recruitment by the host organization) : in the first four years (full-time equivalent) of their research careers and not yet have been awarded a doctoral degree. This is measured from the date when they obtained the degree which would formally entitle them to embark on a doctorate, either in the country in which the degree was obtained or in the country in which the research training is provided, irrespective of whether or not a doctorate is envisaged.

- At the time of recruitment by the host organization, researchers must not have resided or carried out their main activity (work, studies, etc) in the country of their host organization for more than 12 months in the 3 years immediately prior to the reference date.

Summary of lab's interests
The lab is interested in proteins structures and conformational changes relevant to their biological function. We use bioinformatics methods and compare results with those of experiments, noticeably through collaborations.

Summary of project
Protein function often involves a change of conformations. The proposed game will start from one protein conformation and the goal will be to reach a target conformation that could be either known from a different structure or a set of distance restraints. The player will be able to deform the protein using normal modes, set of coordinated movements represented as arrows. He/she would need to choose modes, direction and amplitude. The improvement of the conformation will be displayed on the screen (i.e.: rmsd, actual vs. target distances). To encourage the user to find low energy path towards the target, the maximal energy of the obtained path will be used to rank users in a contest. The paths obtained by all the players will be analysed globally, with tools from FRIAS, to construct the energy landscape.

Interdisciplinarity of the project
The project involves computational tools that need to be developed to study proteins that are biochemisrty/biophysics objects. The tools will have to be usable by diverse audiences: experimentalists, students and the general public.