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Section: Application Domains

Keywords : Molecules, docking.

Algorithmic issues in Structural Biology

Two of the most prominent challenges of the post-genomic era are to understand the molecular machinery of the cell and to develop new drug design strategies. These key challenges require the determination, understanding and exploitation of the three-dimensional structure of several classes of molecules (nucleic acids, proteins, drugs), as well as the elucidation of the interaction mechanisms between these molecules.

These challenges clearly involve aspects from biology, chemistry, physics, mathematics and computer science. For this latter discipline, while the historical focus has been on text and pattern matching related algorithms, the amount of structural data now available calls for geometric methods. At a macroscopic scale, the classification of protein shapes, as well as the analysis of molecular complexes requires shape description and matching algorithms. At a finer scale, molecular dynamics and force fields require efficient data-structures to represent solvent models, as well as reliable meshes so as to solve the Poisson-Boltzmann equation.

Figure 1. (a) Molecular surface (b) A small peptide surrounded by its interface [56]


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