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

Andras Fiser; Zsuzsanna Dosztanyi; Istvan Simon

doi:10.1093/bioinformatics/13.3.297

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

Andras Fiser, Zsuzsanna Dosztanyi, Istvan Simon

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	297-301
Number of pages	5
Journal	Bioinformatics
Volume	13
Issue number	3
DOIs	https://doi.org/10.1093/bioinformatics/13.3.297
State	Published - 1997
Externally published	Yes

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/13.3.297

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title = "The role of long-range interactions in defining the secondary structure of proteins is overestimated",

abstract = "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.",

author = "Andras Fiser and Zsuzsanna Dosztanyi and Istvan Simon",

note = "Funding Information: We thank Drs Miklos Cserzb, Peter Tompa and Gabor Tusnady for critical review of the manuscript. The authors are grateful to Dr Finkelstein for providing the ALB prediction program. This work was supported by the OTKA F017645, TO 12890 and TO 17652 grants.",

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doi = "10.1093/bioinformatics/13.3.297",

language = "English (US)",

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T1 - The role of long-range interactions in defining the secondary structure of proteins is overestimated

AU - Fiser, Andras

AU - Dosztanyi, Zsuzsanna

AU - Simon, Istvan

N1 - Funding Information: We thank Drs Miklos Cserzb, Peter Tompa and Gabor Tusnady for critical review of the manuscript. The authors are grateful to Dr Finkelstein for providing the ALB prediction program. This work was supported by the OTKA F017645, TO 12890 and TO 17652 grants.

PY - 1997

Y1 - 1997

N2 - 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.

AB - 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.

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

Abstract

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