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© Oxford University Press

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

András Fiser , Zsuzsanna Dosztányi and István Simon 1

Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences H-1518 Budapest, PO Box 7, Hungary

1 To whom correspondence should be addressed

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.

Received on October 7, 1996; revised on December 15, 1996; accepted on December 19, 1996

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