title: DOMIRE: a web server for identifying structural domains and their neighbors in proteins.
abstract: CONCLUSIONS
  The DOMIRE web server implements a novel, automatic, protein structural domain assignment procedure based on 3D substructures of the query protein which are also found within structures of a non-redundant protein database. These common 3D substructures are transformed into a co-occurrence matrix that offers a global view of the protein domain organization. Three different algorithms are employed to define structural domain boundaries from this co-occurrence matrix. For each query, a list of structural neighbors and their alignments are provided. DOMIRE, by displaying the protein structural domain organization, can be a useful tool for defining protein common cores and for unravelling the evolutionary relationship between different proteins.
  
  
  BACKGROUND
  http://genome.jouy.inra.fr/domire
  
  
  BACKGROUND
  jean.garnier@jouy.inra.fr.
authors.affiliation: Institut National de la Recherche Agronomique, UR1077, Unité Mathématique, Informatique et Génome, 78350 Jouy-en-Josas, France.
authors.forename: Franck
authors.initials: F
authors.lastname: Samson
authors.forename: Richard
authors.initials: R
authors.lastname: Shrager
authors.forename: Chin-Hsien
authors.initials: CH
authors.lastname: Tai
authors.forename: Vichetra
authors.initials: V
authors.lastname: Sam
authors.forename: Byungkook
authors.initials: B
authors.lastname: Lee
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Munson
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Gibrat
authors.forename: Jean
authors.initials: J
authors.lastname: Garnier
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins