The role of long-range interactions in defining the secondary structure of proteins is overestimated

Comput Appl Biosci. 1997 Jun;13(3):297-301. doi: 10.1093/bioinformatics/13.3.297.


Motivation: 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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Cluster Analysis
  • Databases, Factual
  • Evaluation Studies as Topic
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Software*


  • Proteins