The SuMo server: 3D search for protein functional sites

Bioinformatics. 2005 Oct 15;21(20):3929-30. doi: 10.1093/bioinformatics/bti645. Epub 2005 Sep 1.


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.

Availability: The web server is freely accessible to academia through and full support is available from MEDIT (


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Imaging, Three-Dimensional / methods*
  • Internet*
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Proteins / analysis
  • Proteins / chemistry*
  • Sequence Analysis, Protein / methods*
  • Software*
  • Structure-Activity Relationship
  • User-Computer Interface*


  • Proteins