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Section: Partnerships and Cooperations

International Initiatives

INRIA Associate Teams

GNAPI

  • Title: Geometric and knowledge-based analysis for Nucleic Acid and Protein dynamics and Interactions

  • INRIA principal investigator: JulieBernauer

  • International Partner:

    • Institution: Stanford University School of Medicine (United States)

    • Laboratory: Computational Structural Biology

  • Duration: 2009 - 2011

  • See also: http://www.lix.polytechnique.fr/~bernauer/EA_GNAPI/

  • Many biological processes of therapeutic interest, such as gene regulation, involve RNA molecules and their interactions with large protein assemblies. Recent high-throughput experiments have yielded insights into mechanisms of these processes but often structural models showing important structural features and interactions are lacking. Using 3D data available for proteins and RNA, we derived knowledge-based potentials to predict protein and nucleic-acid 3D structure. In combination with appropriate geometric representations, we obtained fast and accurate all-atom and coarse-grained predictions of biomolecular structures. We show that we can accurately build knowledge-based potentials from various all-atom and coarse-grained measures. Using this method and an encoding of multi-body contacts through arrangement of circles on a sphere, we obtained a reasonable model of protein structure. We also applied this strategy to assess RNA structures and showed that it is currently one of the best performing potentials for RNA structure evaluation. These results suggest that our knowledge-based models may also be suitable for the study of RNA dynamics and interactions.

Visits of International Scientists

Invited researchers (long stays)

  • Peter Clote

    • Subject: Digiteo chair

    • Institution: Boston College (United States of America)

Invited researchers (Short stays)

  • Artem Kasyanov, (IOGene, Moscow), 2 weeks;

    • Institution:IOGene (Russia (Russian Federation))

  • M. Levitt, 3 days

    • Institution: Stanford University (USA)

  • A. Sim(Stanford), 10 days;

    • Institution: Stanford University (USA)

Internship

  • Leonid Uroshlev

    • Subject: Study of reference states for the building of RNA knowledge-based potentials

    • Institution: Laboratoire Franco-Russe Poncelet (Russia (Russian Federation))

  • Angela Yen

    • Subject: A dynamic-programming extension of MC-Fold applicable to Boltzmann equilibrium applications.

    • Institution: MIT (United States of America)

  • Anindya Jyoti Roy

    • Subject: Development of new support vector machines techniques for the analysis of RNA motifs

    • Institution: IIT Kanpur

Participation In International Programs

Exists a long term collaboration between Amib and IoGene , previously NIIGenetika , through Liapunov Institute, former MIGEC associate team and Poncelet Institute.