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Bioinformatics. 2018 Feb 1;34(3):445-452. doi: 10.1093/bioinformatics/btx590.

A comprehensive assessment of long intrinsic protein disorder from the DisProt database.

Author information

1
Department of Biomedical Sciences, University of Padua, 35131 Padova, Italy.
2
Agricoltural Sciences, University of Udine, 33100 Udine, Italy.
3
MTA-ELTE Lendület Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.
4
Fondazione Edmund Mach, 38010 S. Michele all'Adige, Italy.
5
Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1518 Budapest, Hungary.
6
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), and Center for Structural Biology (CSB), Flanders Institute for Biotechnology (VIB), Brussels 1050, Belgium.
7
CNR Institute of Neuroscience, 35131 Padova, Italy.

Abstract

Motivation:

Intrinsic disorder (ID), i.e. the lack of a unique folded conformation at physiological conditions, is a common feature for many proteins, which requires specialized biochemical experiments that are not high-throughput. Missing X-ray residues from the PDB have been widely used as a proxy for ID when developing computational methods. This may lead to a systematic bias, where predictors deviate from biologically relevant ID. Large benchmarking sets on experimentally validated ID are scarce. Recently, the DisProt database has been renewed and expanded to include manually curated ID annotations for several hundred new proteins. This provides a large benchmark set which has not yet been used for training ID predictors.

Results:

Here, we describe the first systematic benchmarking of ID predictors on the new DisProt dataset. In contrast to previous assessments based on missing X-ray data, this dataset contains mostly long ID regions and a significant amount of fully ID proteins. The benchmarking shows that ID predictors work quite well on the new dataset, especially for long ID segments. However, a large fraction of ID still goes virtually undetected and the ranking of methods is different than for PDB data. In particular, many predictors appear to confound ID and regions outside X-ray structures. This suggests that the ID prediction methods capture different flavors of disorder and can benefit from highly accurate curated examples.

Availability and implementation:

The raw data used for the evaluation are available from URL: http://www.disprot.org/assessment/.

Contact:

silvio.tosatto@unipd.it.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28968848
DOI:
10.1093/bioinformatics/btx590
[Indexed for MEDLINE]

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