Web site:

• INSERM
  
• Université Pierre et Marie Curie
  

 

Context

2ptc protein complex : bovine trypsin protease and inhibitor.

This project aims to develop computing tools able to locate on the surface of proteins, interaction sites with DNA, ligands, and other proteins. This development brings together the "Joint Evolutionary Trees" method (inspired by the "Evolutionary Trace" method) and the "Molecular docking" method. The first method is based on the analysis of the evolution of a protein sequence to detect the parts of a protein that are likely to be of biological importance and therefore conserved during evolution. The second method consists of studying the interactions of two 3D protein models, in order to find the spatial positions with correct interactions. In terms of computation time, the algorithms used are very expensive and if hundreds or thousands of proteins need to be analysed the time can amount to centuries. When only the most relevant parts of the protein have been screened, the computation time becomes feasible with a computing power such as Decrypthon's.

Potential map, obtained after docking of the inhibitor on trypsin. (theta and phi angles locate the position of the ligand around trypsin), the ligand position in the crystallographic complex is in the middle of the picture (corresponds to an energetic minimum).

 

 

Interaction sites between the protease and its inhibitor, detected by Joint Evolutionary Trees.

The number of positions to compute for a couple of proteins can be very large and when there is thousands of couples to explore, it could be realized in parallel.

Use case

Initiated in 2001 and relaunched in 2005 by the AFM and IBM in association with the CNRS, Decrypthon is a technology platform providing the computational power required to process complex data in biology today, whose volume is multiplied by two every year. This thus allows, through technologies called “grids”, to gather (in a grid) the capacity of several supercomputers (500 Gflop) installed by IBM in 6 French universities (Bordeaux 1, Lille 1, Paris 6 Jussieu, ENS Lyon, Crihan in Rouen, Orsay) and/or individual personal computers via the World Community Grid (World Community Grid). A dozen scientific projects selected through a call for tenders have been completed under the Decrypthon program.

Contribution

DIET (the free version of SysFera-DS) allows the execution of parallel computations on the entire Decrypthon grid, by interfacing with the local batch schedulers (Loadleveler, OAR). Thus the resources of the "university grid" can be used while allowing them to be shared with the local users when they're not used by the Decrypthon project. A WebBoard interface gives transparency of the grid to the users.

Technical Form

Type	Valeur
Code	Sequential
CPU itensive	Medium
I/O intensive	Low
Memory intensive	High
Plug-in scheduler	No
SysFera-DS Client/Server	Available
Deployment	Decrypthon University Grid

Reference

• HELP CURE MUSCULAR DYSTROPHY
• N. Bard, R. Bolze, E. Caron, F. Desprez, M. Heymann, A. Friedrich, L. Moulinier, N.-H. Nguyen, O. Poch, and T. Toursel. Décrypthon Grid - Grid Resources Dedicated to Neuromuscular Disorders. In The 8th HealthGrid conference, Paris, France, June 2010.