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

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

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, sugge...

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Main Authors: Éva Tüdős, Bálint Mészáros, András Fiser, István Simon
Format: Article
Language:English
Published: Wiley 2014-01-01
Series:FEBS Open Bio
Subjects:
Protein prediction
Cysteine redox state
Protein structure
Prediction accuracies
Biological inference
Online Access:http://www.sciencedirect.com/science/article/pii/S2211546314000266
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spelling doaj-dbbf6d8fdfa346ecb04e6f3245ae40d42020-11-25T03:59:16ZengWileyFEBS Open Bio2211-54632014-01-014C31031410.1016/j.fob.2014.03.003A word of caution about biological inference – Revisiting cysteine covalent state predictionsÉva Tüdős0Bálint Mészáros1András Fiser2István Simon3Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 286, H-1519 Budapest, HungaryInstitute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 286, H-1519 Budapest, HungaryDepartment of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461, USAInstitute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, P.O. Box 286, H-1519 Budapest, HungaryThe 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.http://www.sciencedirect.com/science/article/pii/S2211546314000266Protein predictionCysteine redox stateProtein structurePrediction accuraciesBiological inference
collection DOAJ
language English
format Article
sources DOAJ
author Éva Tüdős
Bálint Mészáros
András Fiser
István Simon
spellingShingle Éva Tüdős
Bálint Mészáros
András Fiser
István Simon
A word of caution about biological inference – Revisiting cysteine covalent state predictions
FEBS Open Bio
Protein prediction
Cysteine redox state
Protein structure
Prediction accuracies
Biological inference
author_facet Éva Tüdős
Bálint Mészáros
András Fiser
István Simon
author_sort Éva Tüdős
title A word of caution about biological inference – Revisiting cysteine covalent state predictions
title_short A word of caution about biological inference – Revisiting cysteine covalent state predictions
title_full A word of caution about biological inference – Revisiting cysteine covalent state predictions
title_fullStr A word of caution about biological inference – Revisiting cysteine covalent state predictions
title_full_unstemmed A word of caution about biological inference – Revisiting cysteine covalent state predictions
title_sort word of caution about biological inference – revisiting cysteine covalent state predictions
publisher Wiley
series FEBS Open Bio
issn 2211-5463
publishDate 2014-01-01
description 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.
topic Protein prediction
Cysteine redox state
Protein structure
Prediction accuracies
Biological inference
url http://www.sciencedirect.com/science/article/pii/S2211546314000266
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