Les complexes protéiques présents dans le docking benchmark v5.5 appartiennent à des groupes fonctionnels et structuraux variés.
Protein interactions play a key role in many cellular processes, such as transport, signaling and immune response. Molecular-scale modeling of protein assemblies traditionally relies on docking software that will generate sets of models of the targeted complex, whose quality will be assessed by comparing these with a single experimental reference structure.
The publication in spring 2021 of the structural prediction software Alpha-Fold2, followed this autumn by Alpha-Fold-Multimer, which is specifically dedicated to the prediction of protein assemblies, has profoundly changed the landscape of structural bioinformatics. Nevertheless, these remarkably efficient tools remain limited to a purely static vision of the objects they describe, whereas we now know that proteins and their complexes are indeed flexible objects, and that the dynamics of the interface between two proteins is a central element of its function.
The aim of the DynaBench project is therefore to decipher and characterize the dynamics at the level of protein interfaces formed by complexes of biological interest. To achieve this, GENCI's exceptional allocation of 90 million CPU hours on Joliot-Curie has enabled Molecular Dynamics calculations to be carried out on all 250 protein complexes that form the Docking-Benchmark 5.5, a reference database for modelers that includes systems
belonging to a variety of functional groups. Analysis of the trajectories thus generated (which will be made available to the scientific community) will make it possible to characterize these interfaces from a dynamic perspective and to better understand, at the atomic scale, how these objects interact in the cell to achieve their biological function.
In 2023, this project is being funded via the Bosphorus CHP in collabo- ration with Turkey.
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