PRABI
Rhone-Alpes Bioinformatics Center


PRABI : IBCP

SuMo

An bioinformatic method to detect similar three-dimensional (3D) sites in proteins

This approach allows the comparison of protein structures or substructures and detects local spatial similarities : this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases.

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Publication : A new bioinformatic approach to detect common 3D sites in protein structures, M Jambon, A Imberty, G Deléage and C Geourjon, 2003, Proteins, 52, 137-145.