title: Structure motif discovery and mining the PDB.
abstract: BACKGROUND
  Many of the most interesting functional and evolutionary relationships among proteins are so ancient that they cannot be reliably detected through sequence analysis and are apparent only through a comparison of the tertiary structures. The conserved features can often be described as structural motifs consisting of a few single residues or Secondary Structure (SS) elements. Confidence in such motifs is greatly boosted when they are found in more than a pair of proteins.
  
  
  RESULTS
  We describe an algorithm for the automatic discovery of recurring patterns in protein structures. The patterns consist of individual residues having a defined order along the protein's backbone that come close together in the structure and whose spatial conformations are similar. The residues in a pattern need not be close in the protein's sequence. The work described in this paper builds on an earlier reported algorithm for motif discovery. This paper describes a significant improvement of the algorithm which makes it very efficient. The improved efficiency allows us to use it for doing unsupervised learning of patterns occurring in small subsets in a large set of structures, a non-redundant subset of the Protein Data Bank (PDB) database of all known protein structures.
authors.affiliation: Department of Informatics, University of Bergen, HIB, N5020 Bergen, Norway. Inge.Jonassen@ii.uib.no
authors.forename: Inge
authors.initials: I
authors.lastname: Jonassen
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
authors.forename: Darrell
authors.initials: D
authors.lastname: Conklin
authors.forename: William R
authors.initials: WR
authors.lastname: Taylor
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology; D003553:Cystine / Q000737:chemistry; D030562:Databases, Protein; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D003553:Cystine