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Equipe de Modélisation
Protein Design in Silico
Picture: Discrete breathers in nonlinear network models of proteins Picture: Docking of oNPGal within the [+1]/[+2] subsites of the A221W mutant Picture: Principe of encoding of protein structures using Structural Alphabet

Group leader: Yves-Henri Sanejouand (DR CNRS).

Present members: Vinh Tran (PU émérite), Bernard Offmann (PU), Téletchéa Stéphane (MCU), Johann Hendrickx (IE CNRS), Lionel Hoffmann (IE CNRS), Mahesh Velusamy (PhD student), Ennys Gheyouche (PhD student), Surbhi Dhingra (PhD student).

Funding sources: national project BIP-BIP; regional projects GRIOTE and PIRAMID.

The two main goals of the Protein Design in Silico team are the following ones:

  1. To help interpreting experimental results obtained by the other teams of UFIP. For this purpose, standard modelisation methods and approaches are usually used (molecular dynamics simulations, protein-protein, protein-ligand docking, etc).
  2. To develop methods for studying the sequence-structure-dynamics-function relationship of proteins, focusing on recent and original approaches (normal mode analysis, structural alphabets...). More specifically:
    1. Sequence­-structure relationship: structural alphabets are developped, focusing noteworthy on the prediction of local and tertiary structures (the fold recognition problem).
    2. Structure-­flexibility relationship: previous work on normal mode analysis is extended, focusing noteworthy on the production of ensembles of protein conformers able to recapitulate the ensembles that can be observed by nuclear magnetic resonance or in the course of long molecular dynamics simulations.
    3. Structure-function relationship: previous work on protein-oligosaccharide (in collaboration with the Glycobiology team) and protein-odorant complexes is extended. The protein-protein recognition issue is also addressed, within the frame of a large regional collaboration (the PIRAMID project).