Biology Reference
In-Depth Information
Chapter 1
SuMo: A Tool for Protein Function Inference
Based on 3D Structures Comparisons
Julie-Anne Chemelle , Emmmanuel Bettler , Christophe Combet ,
Raphaël Terreux , Christophe Geourjon , and Gilbert Deléage
Abstract
The prediction of important residues for binding/recognition sites in
protein 3D structures is still a matter of challenge. Indeed, binding sites recognition
is generally based on geometry often combined with physico-chemical properties
of the site since the conformation, size and chemical composition of the protein
surface are all relevant for the interaction with a specific ligand. In our group, we
designed an innovative bioinformatics method called SuMo in order to detect similar
3-dimensional (3D) sites in proteins (Jambon et al. Protein-Struct Funct Genet
52:137-145, 2003). This approach allowed the comparison of protein structures or
substructures, and detected local spatial similarities: the main advantage of the
method is its independence for both amino acid sequences and backbone structures.
In contrast to already existing tools, the basis for this method is a representation of
the protein structure by a set of stereo chemical groups that are defined indepen-
dently from the notion of amino acid. An efficient heuristics for finding similarities
has been developed which uses graphs of triangles of chemical groups to represent
the protein structures. The SuMo (Surfing the Molecules) program allows the dynamic
definition of chemical groups, the selection of sites in the proteins, and the man-
agement and screening of databases. The basic principle of SuMo has been used in
several recent studies (Sperandio et al. J Cheml Inf Model 47:1097-1110, 2007)
J.-A. Chemelle • E. Bettler • C. Combet • R. Terreux • C. Geourjon • G. Deléage (
*
)
Université Lyon 1, CNRS, UMR 5086; Bases Moléculaires et Structurales des Systèmes
Infectieux , Lyon , France
e-mail: gilbert.deleage@ibcp.fr
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