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Nature Research, Nature Methods, 5(18), p. 472-481, 2021

DOI: 10.1038/s41592-021-01117-3

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Critical assessment of protein intrinsic disorder prediction

Journal article published in 2021 by Ian Walsh, Chen Wang, Yaoqi Zhou, Björn Wallner, Kui Wang, Zhonghua Wu, Jinbo Xu, Sheng Wang, Jing Yan, Tianqi Wu, Lucía Álvarez, Michele Vendruscolo, Salvador Ventura, Nevena Veljkovic, E. Tosatto Silvio C. and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

AbstractIntrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the state of the art in prediction of intrinsically disordered regions and the subset of residues involved in binding. A total of 43 methods were evaluated on a dataset of 646 proteins from DisProt. The best methods use deep learning techniques and notably outperform physicochemical methods. The top disorder predictor has Fmax = 0.483 on the full dataset and Fmax = 0.792 following filtering out of bona fide structured regions. Disordered binding regions remain hard to predict, with Fmax = 0.231. Interestingly, computing times among methods can vary by up to four orders of magnitude.