March 2020, Sorbonne Université in Paris allies with several computational scientists in France and across the globe to study the molecular structure of COVID19 in collaboration with Institut Pasteur, a world leading institute in emerging infectious diseases.
In an urge to understand the molecular structure of the virus, over thirty worldwide scientists from six renowned institutions (Sorbonne Université, Conservatoire National des Arts et Métiers, Université de Limoges, University of Texas at Austin, University of North-Texas and Washington University in Saint Louis) lead by Jean-Philip Piquemal are collaborating to simulate and target the functional proteins of the COVID19 virus. Such computer models will help scientists to design new drugs able to neutralize the coronavirus by preventing it from entering human cells or by blocking its internal machinery.
Display of the Spike (S) virus protein which plays a key role into the Covid-19 entrance into the human cells. The picture is extracted from HPC simulations performed by the Sorbonne University team using the Jean Zay supercomputer and the Tinker-HP software (picture credit: Université de Limoges/CNAM, VTX visualization software)
Display of the Spike (S) protein interacting with the human ACE-2 cellular receptor (in grey). The picture is extracted from HPC simulations performed by the Sorbonne University team using the Jean Zay supercomputer and the Tinker-HP software (picture credit: Université de Limoges/CNAM, VTX
Researchers are relying on an urgent-computing access mode to the most performant European converged HPC and AI operational supercomputer called “Jean Zay” (16 PFlop/s) and the fastest existing massively parallel multi-GPU approach Tinker-HP. Running on Jean Zay supercomputer, Tinker-HP software solution, optimized by HPE, IDRIS and the developers team, offers a high-performance computing environment providing access to the modeling of complex systems of up to millions of atoms. It is the fastest approach currently available to perform state-of-the-art molecular dynamics simulations with high-resolution polarizable energy model allowing to capture viral infection mechanisms in most realistic details.
(Crédits Cyril FRESILLON / IDRIS / CNRS Photo library)
The Jean Zay supercomputer designed by HPE (Hewlett Packard Enterprise) and inaugurated in January 2020 was acquired by GENCI (Grand Equipement National de Calcul Intensif), the French HPC agency, and is operated within the IDRIS (Institut du Développement et des Ressources en Informatique Scientifique), the largest center for Artificial Intelligence and numerical simulation of CNRS (Centre National de Recherche Scientifique).
- Group of Prof. J-P Piquemal (ERC EMC2, grant agreement No 810367), LCT, UMR 7616 CNRS, Sorbonne Université, Paris, France
- Group of Prof. M. Montes (ERC ViDock, grant agreement 640283), GBCM, CNAM, Hésam Université, Paris, France
- Group of Dr. M. Maria, XLIM,UMR 7252 CNRS, Université de Limoges, France
- Group of Dr. M. Nilges, Structural Bioinformatics, UMR 3528 CNRS, Institut Pasteur, Paris, France
- Group of Prof. P. Ren, Dept of Biomedical Engineering, University of Texas at Austin, TX, USA
- Group of Prof. J. W. Ponder, Dept of Chemistry, Washington University in Saint Louis, MO, USA
- Group of Prof. G. A. Cisneros, Dept of Chemistry, University of North Texas, TX, USA