The SuMo server: 3D search for protein functional sites

• DOI: 10.1093/bioinformatics/bti645
• Publication Date: 2005-09-03T00:14:12Z
• Authors: M. Jambon; O. Andrieu; C. Combet; G. Deleage; F. Delfaud; C. Geourjon
• Keywords: 0301 basic medicine; MESH: Sequence Analysis, Protein; Protein Conformation; Molecular Sequence Data; MESH: Amino Acid Sequence; MESH: Imaging, Three-Dimensional; MESH: Software; Structure-Activity Relationship; User-Computer Interface; 03 medical and health sciences; MESH: Structure-Activity Relationship; MESH: Protein Conformation; Imaging, Three-Dimensional; Sequence Analysis, Protein; Protein Interaction Mapping; MESH: Protein Binding; MESH: Proteins; [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology; Amino Acid Sequence; MESH: User-Computer Interface; Internet; MESH: Molecular Sequence Data; Binding Sites; MESH: Protein Interaction Mapping; Proteins; MESH: Internet; MESH: Binding Sites; Software; Protein Binding

We provide the scientific community with a web server which gives access to SuMo, a bioinformatic system for finding similarities in arbitrary 3D structures or substructures of proteins. SuMo is based on a unique representation of macromolecules using selected triplets of chemical groups having their own geometry and symmetry, regardless of the restrictive notions of main chain and lateral chains of amino acids. The heuristic for extracting similar sites was used to drive two major large-scale approaches. First, searching for ligand binding sites onto a query structure has been made possible by comparing the structure against each of the ligand binding sites found in the Protein Data Bank (PDB). Second, the reciprocal process, i.e. searching for a given 3D site of interest among the structures of the PDB is also possible and helps detect cross-reacting targets in drug design projects.The web server is freely accessible to academia through http://sumo-pbil.ibcp.fr and full support is available from MEDIT (http://www.medit.fr)[e-mail].