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

András Fiser, Z. Dosztányi, I. Simon

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Motivation: Secondary 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.

Original languageEnglish
Pages (from-to)297-301
Number of pages5
JournalComputer Applications in the Biosciences
Volume13
Issue number3
Publication statusPublished - 1997

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Structure Collapse
Secondary Protein Structure
Long-range Interactions
Secondary Structure
Structure Prediction
Proteins
Protein
Nonlocal Interactions
Local Interaction
Set theory
Exceed
Subset
Prediction
Alternatives

ASJC Scopus subject areas

  • Medicine (miscellaneous)

Cite this

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AB - Motivation: Secondary 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.

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