A word of caution about biological inference - Revisiting cysteine covalent state predictions

Éva Tüdos; Bálint Mészáros; András Fiser; István Simon

doi:10.1016/j.fob.2014.03.003

A word of caution about biological inference - Revisiting cysteine covalent state predictions

Éva Tüdos, Bálint Mészáros, András Fiser, István Simon

Systems & Computational Biology

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

1 Scopus citations

Abstract

The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools.

Original language	English (US)
Pages (from-to)	310-314
Number of pages	5
Journal	FEBS Open Bio
Volume	4
DOIs	https://doi.org/10.1016/j.fob.2014.03.003
State	Published - 2014

Keywords

Biological inference
Cysteine redox state
Prediction accuracies
Protein prediction
Protein structure

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

Access to Document

10.1016/j.fob.2014.03.003

Cite this

@article{156c05dd219a4d2ab9b72e5ea5c556ea,

title = "A word of caution about biological inference - Revisiting cysteine covalent state predictions",

abstract = "The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools.",

keywords = "Biological inference, Cysteine redox state, Prediction accuracies, Protein prediction, Protein structure",

author = "{\'E}va T{\"u}dos and B{\'a}lint M{\'e}sz{\'a}ros and Andr{\'a}s Fiser and Istv{\'a}n Simon",

note = "Funding Information: We thank Drs. Zs. Doszt{\'a}nyi, Cs. Magyar and G. E. Tusn{\'a}dy for the critical reading of the manuscript. This work was supported by research grants OTKA NK 100482 and NIH GM096041 and NIH U54GM094662 . ",

year = "2014",

doi = "10.1016/j.fob.2014.03.003",

language = "English (US)",

volume = "4",

pages = "310--314",

journal = "FEBS Open Bio",

issn = "2211-5463",

publisher = "Elsevier BV",

}

TY - JOUR

T1 - A word of caution about biological inference - Revisiting cysteine covalent state predictions

AU - Tüdos, Éva

AU - Mészáros, Bálint

AU - Fiser, András

AU - Simon, István

N1 - Funding Information: We thank Drs. Zs. Dosztányi, Cs. Magyar and G. E. Tusnády for the critical reading of the manuscript. This work was supported by research grants OTKA NK 100482 and NIH GM096041 and NIH U54GM094662 .

PY - 2014

Y1 - 2014

N2 - The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools.

AB - The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools.

KW - Biological inference

KW - Cysteine redox state

KW - Prediction accuracies

KW - Protein prediction

KW - Protein structure

UR - http://www.scopus.com/inward/record.url?scp=84897423343&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84897423343&partnerID=8YFLogxK

U2 - 10.1016/j.fob.2014.03.003

DO - 10.1016/j.fob.2014.03.003

M3 - Article

AN - SCOPUS:84897423343

SN - 2211-5463

VL - 4

SP - 310

EP - 314

JO - FEBS Open Bio

JF - FEBS Open Bio

ER -

A word of caution about biological inference - Revisiting cysteine covalent state predictions

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this