title: Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.
abstract: BACKGROUND
  Today, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software.
  
  
  RESULTS
  In this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function.
  
  
  CONCLUSIONS
  The possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.
authors: Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors: Maria U
authors: MU
authors: Johansson
authors: Vincent
authors: V
authors: Zoete
authors: Olivier
authors: O
authors: Michielin
authors: Nicolas
authors: N
authors: Guex
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D030562:Databases, Protein; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins