Contributions au développement d’outils computationnels de design de protéines : méthodes et algorithmes de comptage avec garantie


Clément Viricel


Université Paul Sabatier (for PhD)


Thomas Schiex, INRA, Toulouse, France
Sophie Barbe, INSA/LISBP, Toulouse, France


This thesis is focused on two intrinsically related subjects : the computation of the normalizing constant of a Markov random field and the estimation of the binding affinity of protein-protein interactions. First, to tackle this #P-complete counting problem, we developed Z ε ∗ , based on the pruning of negligible potential quantities. It has been shown to be more efficient than various state-of-the-art methods on instances derived from protein-protein interaction models. Then, we developed #HBFS, an anytime guaranteed counting algorithm which proved to be even better than its predecessor. Finally, we developed BTDZ, an exact algorithm based on tree decomposition. BTDZ has already proven its efficiency on intances from coiled coil protein interactions. These algorithms all rely on methods stem- ming from graphical models : local consistencies, variable elimination and tree decomposition. With the help of existing optimization algorithms, Z ε ∗ and Rosetta energy functions, we developed a package that estimates the binding affinity of a set of mutants in a protein-protein interaction. We statistically analyzed our esti- mation on a database of binding affinities and confronted it with state-of-the-art methods. It appears that our software is qualitatively better than these methods.