title: Quantitative method for the assignment of hinge and shear mechanism in protein domain movements.
abstract: BACKGROUND
  A popular method for classification of protein domain movements apportions them into two main types: those with a 'hinge' mechanism and those with a 'shear' mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term 'shear' is often interpreted to mean a relative translation of the domains.
  
  
  RESULTS
  Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms.
  
  
  METHODS
  Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/.
  
  
  BACKGROUND
  sjh@cmp.uea.ac.uk.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors: Daniel
authors: D
authors: Taylor
authors: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors: Gavin
authors: G
authors: Cawley
authors: D'Arcy Thompson Centre for Computational Biology, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
authors: Steven
authors: S
authors: Hayward
mesh_terms: D016015:Logistic Models; D009038:Motion; D017434:Protein Structure, Tertiary; D012399:Rotation; D012984:Software