Section: Partnerships and Cooperations

National Initiatives

Projets Exploratoires Pluridisciplinaires from CNRS/Inria/INSERM

• Title: Novel approaches to characterizing flexible macromolecular systems in biology

  Modeling Large Protein Assemblies with Toleranced Models

• Type: Projet Exploratoire Pluri-disciplinaire (PEPS) CNRS / Inria / INSERM

• Duration: one year

• Coordinator: C. Robert (IBPC / CNRS)

• Other partner(s): F. Cazals (Inria Sophia Antipolis Méditerranée)

• Abstract: A central problem in structural biology consists of modeling the dynamics and thermodynamics of macro-molecular assemblies involving a large number of atoms (thousands to hundreds of thousands). This requires understanding the structure of the potential and free energy landscapes (PEL and FEL) of the system. A number of approaches have been developed from the physical perspective, in particular to sample the PEL of the systems scrutinized (molecular dynamics, Monte Carlo based methods). The goal of this project is orthogonal, since our aim is to enhance the processing of samplings generated by the aforementioned approaches. Our methods aim at analyzing and comparing sampled PEL and FEL, using novel methods from computational geometry, computational topology, and optimization. These methods should foster our understanding of the behavior of macro-molecular assemblies, and in the long run, they should also trigger the development of more efficient sampling algorithms.