Stamps, functional topology search through protein 3D structures.

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.