Critical assessment of protein intrinsic disorder prediction
By Marco Necci, Damiano Piovesan, Md. Tamjidul Hoque, Ian Walsh, S. Iqbal, Michele Vendruscolo, Pietro Sormanni, Chen Wang, Daniele Raimondi, Ronesh Sharma and 88 more. 2020
286 citations recorded by the source corpus.
Intrinsically 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. Results are presented from the first Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment, a community-based blind test to determine the state of the art in predicting intrinsically disordered regions in proteins.
Subfields: Molecular Biology
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In Molecular Biology
- Gábor Erdös
- Zsuzsanna Dosztányi
- Tommi S. Jaakkola
- Regina Barzilay
- Damiano Piovesan
- Hannes Stärk
- Silvio C. E. Tosatto
- Bowen Jing
Citations in the corpus
- Critical assessment of protein intrinsic disorder prediction (CAID) ‐ Results of round 2 (2023, background): “The Critical Assessment of Protein Intrinsic Disorder Prediction (CAID) 5 focuses on analyzing the simpler problem of identifying positions within the protein sequence that have a propensity for being intrinsically disordered.”
- DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking (2022, background): “[18] Marco Necci, Damiano Piovesan, and Silvio CE Tosatto.”
- IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation (2021, methodology): “Recently, a Critical Assessment of protein Intrinsic Disorder (CAID) prediction experiment was launched as a community-based blind test to determine the state of the art in predicting intrinsically disordered regions (15).”
- Intrinsic protein disorder and conditional folding in AlphaFoldDB (2022, methodology): “As previously noted, this definition suggests that intrinsic disorder can be considered the opposite of globular structure.(13) When using the DisProt definition, the situation changes somewhat (see Figure 2b, Tables S3 and S4), with AlphaFold-RSA being among the top five methods.”