title: Identification of function-associated loop motifs and application to protein function prediction.
abstract: BACKGROUND
  The detection of function-related local 3D-motifs in protein structures can provide insights towards protein function in absence of sequence or fold similarity. Protein loops are known to play important roles in protein function and several loop classifications have been described, but the automated identification of putative functional 3D-motifs in such classifications has not yet been addressed. This identification can be used on sequence annotations.
  
  
  RESULTS
  We evaluated three different scoring methods for their ability to identify known motifs from the PROSITE database in ArchDB. More than 500 new putative function-related motifs not reported in PROSITE were identified. Sequence patterns derived from these motifs were especially useful at predicting precise annotations. The number of reliable sequence annotations could be increased up to 100% with respect to standard BLAST.
  
  
  BACKGROUND
  boliva@imim.es
  
  
  BACKGROUND
  Supplementary Data are available at Bioinformatics online.
authors.affiliation: Group de Bioinformàtica Estructural (GRIB-IMIM), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra 08003 Barcelona, Catalonia, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Espadaler
authors.forename: Enrique
authors.initials: E
authors.lastname: Querol
authors.forename: Francesc X
authors.initials: FX
authors.lastname: Aviles
authors.forename: Baldo
authors.initials: B
authors.lastname: Oliva
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins