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ABS Research team

Algorithms, Biology, Structure

Team presentation

The research activity of ABS (Algorithms, Biology, Structure) lies at the interface of Computer Science and Structural Biology. The central underlying problem being the elucidation of the relationship between the structure and the function of macro-molecules, two questions emerge: the prediction of the structure of a protein from its amino-acid sequence (folding), and the prediction of the structure of a complex from unbound molecules (docking). These questions face two classes of difficulties. First, a macro-molecular system features a large number of degrees of freedom ---three per atom to scale things. Second, the relevant timescales span a wide spectrum: while the integration time-step used in Molecular Dynamics simulations is the femtosecond, biological time-scales are beyond the second.

In this context, multi-scale approaches are a must, and for a particular problem, the methods used depend on the accuracy sought. Coarse methods, often used during exploratory phases, are essentially of geometric nature, and involve supervised learning on databases featuring biological and fake structures. Given the limited precision of such models, a large number of structures is usually dealt with. Finer strategies are based on more precise physical models and force fields, and usually involve explicit solvent molecules. Locating the minima of energy of such systems poses difficult optimisation problems.

The goals of ABS span these modeling scales, and are geared towards a better understanding of macro-molecular systems based on the development of more accurate models, and also of algorithms handling more efficiently and reliably such models. In the long run, these works are expected to contribute to the integration of structural informations in systems biology.

Research themes

  • Modeling atomic resolution protein complexes.
  • Modeling large protein assemblies.
  • Modeling the flexibility of proteins.
  • Algorithmic foundations.
  • Software.

International and industrial relations

  • J. Janin, CNRS / Orsay
  • C.H. Robert, IBPC / CNRS, Paris

Keywords: Structural Biology - Computational Biology Proteins Folding Docking Complexes