Symbiose Project Team - INRIA/Irisa © 2007 - 2008

Jeudi 31 Mars, guilllaume Collet, CEA Saclay
Written by Pierre PETERLONGO   

Stamps, functional topology search through protein 3D structures.

10h30 salle Aurigny

The design of articial protein ligands able to interact with receptors is a formidable goal to understand the fundamental basis of ligand-receptor interactions, which is inferred to lead to discover of novel therapeutics. We have developed a structure-based approach to design articial protein ligand (or articial enzymes), based on the transfer of a functional binding motif of amino acids on a host protein able to reproduce the functional 3D-topology of these amino acids.
Our application, STAMPS, consists in a systematic search of a functional topology of amino acids through the 3D structures of proteins available in the public Protein Data Bank (containing about 70 000 structures, in a on going exponential growth). STAMPS considers the atom-atom distances of the functional motif and iteratively compares this set of distances to all atom-atom distances of the 3D structures, which corresponds to an embarrassingly parallel computational task.

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