Molecular simulations allow researchers to obtain complementary data with respect to experimental studies and to overcome some of their limitations. Current experimental techniques do not allow to observe the full dynamics of a protein at atomic detail. In return, experiments provide the structures, i.e. the spatial atomic positions, for numerous biomolecular systems, which are often used as starting point for simulation studies. In order to predict, to explain and to understand experimental results, researchers have developed a variety of biomolecular representations and algorithms. […]

A. Tek, B. Laurent, M. Piuzzi, Z. Lu, M. Baaden, O. Delalande, M. Chavent, N. Férey, C. Martin, L. Piccinali, B. Katz, P. Bourdot, Ludovic Autin ; Advances in Human-Protein Interaction - Interactive And Immersive Molecular Simulations ; W. Cai and H. Hong ; Intech, CroatiaRead more...

We are seeking a highly motivated candidate to design and implement a next generation visualization platform for analysis of large-scale molecular simulations. In particular, we target two grand challenge applications: modeling a complete influenza virus and analyzing extensive simulations of the GLIC receptor that we recently published in the journals Nature and PNAS. The foundations for this project were previously established within the FvNano project, providing a well defined framework to get started. Using visual analytics approaches and high performance interactive graphics, you will implement readily usable state-of-art tools scaling up to the next generation of simulations. This position is a unique training opportunity in a multi-disciplinary environment in collaboration with four other leading teams in France who are experts on complementary topics, and two international partners in the U.K. and in Germany.

PDF-page of this job offer and general background: http://exaviz.simlab.ibpc.fr
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Balises : Visualization, InEnglish, jobs

The FvNano project officially ended on 31 december 2011. We are currently updating the webpages because the project still produces output in the form of publications, posters, websites and code that can be downloaded and tested. Have a look at the FvNano webpage for the latest details.
FVNano-related research will continue in the ExaViz project about exa-scalable visual analysis for life & materials sciences. ExaViz already has its own website with a job section and several offers. An overall description of the project and the teams involved is also provided.

Balises : research, Visualization, InEnglish

We investigate the conformational dynamics and mechanical properties of guanylate kinase (GK) using a multiscale approach combining high-resolution atomistic molecular dynamics and low-resolution Brownian dynamics simulations. The GK enzyme is subject to large conformational changes, leading from an open to a closed form, which are further influenced by the presence of nucleotides. As suggested by recent work on simple coarse-grained models of apo-GK, we primarily focus on GK's closure mechanism with the aim to establish a detailed picture of the hierarchy and chronology of structural events essential for the enzymatic reaction. We have investigated open-versus-closed, apo-versus-holo, and substrate-versus-product-loaded forms of the GK enzyme. Bound ligands significantly modulate the mechanical and dynamical properties of GK and rigidity profiles of open and closed states hint at functionally important differences. Our data emphasizes the role of magnesium, highlights a water channel permitting active site hydration, and reveals a structural lock that stabilizes the closed form of the enzyme.
By Olivier Delalande, Sophie Sacquin-Mora and Marc Baaden, published in Biophysical Journal Volume 101, Issue 6, 1440-1449, 21 September 2011.

Balises : research, InEnglish

Welcome to Samuel Murail, Francesco Oteri and Antoine Taly who have just arrived in the lab. Samuel will be working as a post-doc on the Nico_chimera project. Francesco is also carrying out post-doctoral research in the BioPac project. Antoine has previously been in Strasbourg and has joined our lab as a CNRS researcher and expert in channels and receptors.

Balises : Labo