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Section: Partnerships and Cooperations
International Initiatives
Inria Associate Teams Not Involved in an Inria International Labs
PPI-3D
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International Partner (Institution - Laboratory - Researcher):
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See also: https://team.inria.fr/nano-d/research/ppi-3d-structure-meets-genomics/
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Protein–protein interactions are integral to many mechanisms of cellular control, and therefore their characterization has become an important task for both experimental and computational approaches in systems biology. Genome-wide proteomics studies provide a growing list of putative protein-protein interactions, and demonstrate that most if not all proteins have interacting partners in the cell. A fraction of these interaction has been reliably established, however, one can only identify whether two proteins interact and, in the best cases, which are the individual domains mediating the interaction. A full comprehension of how proteins bind and form complexes can only come from high-resolution three-dimensional structures. While the most complete structural characterization of a complex is provided by X-ray crystallography, protein-protein hetero-complexes constitute less than 6%§ of protein structures in the Protein Data Bank. Thus, it is important to develop computational methods that, starting from the structures of component proteins, can determine the structure of their complexes.
The basic problem of predictive protein docking is to start with the structures (or sequences) of unbound component proteins A and B, and to obtain computationally a model of the bound complex AB, as detailed structural knowledge of the interactions facilitates understanding of protein function and mechanism. Our current docking approaches performs ab initio docking of the two structures without the use of any additional information. The goal of this proposal is to speed up docking approaches to tackle genome-scale problems, and utilize additional information on interactions, sequences, and structures that is available for virtually any protein.
This project includes several methodological and application research directions: 1) Developing fast sampling approaches; 2) Development of new scoring functions; 3) Integrative approaches for structure determination.
Overall, during the course of the project we will (i) jointly develop new methodology and algorithms in the field of genomic-scale protein complex prediction; (ii) provide server-based applications built upon services of the Boston team; (iii) and finally develop modular applications coded inside the SAMSON software platform created by the Inria team.