title: The role of long-range interactions in defining the secondary structure of proteins is overestimated.
abstract: BACKGROUND
  Secondary structure predictions based on the properties of individual residues, and sometimes on local interactions, usually fail to exceed 65% efficiency. Therefore, non-local, long-range interactions seem to be a significant cause of this limitation.
  
  
  RESULTS
  In this paper, we apply approaches to localize highly interacting residues and clusters of residues involved in multiple non-local interactions, and test various secondary structure predictions on this separate subset to assess the effect of long-range interactions on the prediction efficiencies. It was found that only a marginal part of the failure of secondary structure predictions results from the presence of long-range interactions. Alternative possibilities are also discussed.
authors.affiliation: Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary. fiser@enzim.hu
authors.forename: A
authors.initials: A
authors.lastname: Fiser
authors.forename: Z
authors.initials: Z
authors.lastname: Dosztányi
authors.forename: I
authors.initials: I
authors.lastname: Simon
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins