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Bioinformatics Advance Access published online on September 1, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti645
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 24, 2005
Revised August 2, 2005
Accepted August 24, 2005

Applications note

The SuMo server: 3D search for protein functional sites

Martin Jambon 1*, Olivier Andrieu 2, Christophe Combet 3, Gilbert Deléage 3, François Delfaud 2, and Christophe Geourjon 3

1 Pôle BioInformatique Lyonnais, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128, 7 passage du Vercors, 69367 Lyon cedex 07, France; present address: The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
2 MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France
3 Pôle BioInformatique Lyonnais, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128, 7 passage du Vercors, 69367 Lyon cedex 07, France

* To whom correspondence should be addressed.
Martin Jambon, E-mail: mjambon{at}burnham.org


  Abstract

Summary: 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 2 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.

Availability: 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).


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