ArticleComputational and structural biotechnology journal2023
Comparative evaluation of AlphaFold2 and disorder predictors for prediction of intrinsic disorder, disorder content and fully disordered proteins.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 31 citations in OpenAlex.
- Functional flexibility in bacterial hub proteins is driven by proteome expansion.Scientific reports · 2026Article
- Shoebill: an interpretable AlphaFold2-informed predictor of protein crystallization propensity using XGBoost.Briefings in bioinformatics · 2026Article
- Generative design of intrinsically disordered protein regions with IDiom.bioRxiv : the preprint server for biology · 2026Article
- Modern resources for intrinsic disorder predictions: protein language models, deep learning, meta-servers, and databases.Cellular and molecular life sciences : CMLS · 2026Review
- Metal-Coordination Specificity and Structural Dynamics of C. elegans Metallothionein I: Insights From 3D Modeling and MD Simulations.Proteins · 2026Article
- Enhancing missense variant classification in predicted intrinsically disordered regions.PloS one · 2026Article
- Functional and Structural Determinants of Long- and Short-Term Evolution of Herpesvirus Proteins.Molecular biology and evolution · 2025Article
- Comparative assessment of binding residue predictions in intrinsically disordered regions.Protein science : a publication of the Protein Society · 2025Article
- Leveraging protein structural information to improve variant effect prediction.Current opinion in structural biology · 2025Review
- Comprehensive assessment of AlphaFold's predictions of secondary structure and solvent accessibility at the amino acid-level in eukaryotic, bacterial and archaeal proteins.Computational and structural biotechnology journal · 2025Article
- Accurate and Fast Prediction of Intrinsic Disorder Using flDPnn.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evaluation of predictions of disordered binding regions in the CAID2 experiment.Computational and structural biotechnology journal · 2025Review
- Taxonomy-specific assessment of intrinsic disorder predictions at residue and region levels in higher eukaryotes, protists, archaea, bacteria and viruses.Computational and structural biotechnology journal · 2024Article
- Survey of the Aβ-peptide structural diversity: molecular dynamics approaches.Biophysical reviews · 2024Review
- An integrative characterization of proline cis and trans conformers in a disordered peptide.Biophysical journal · 2024Article
- The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins.Nature chemical biology · 2024Review
- Characterization of alternative splicing during mammalian brain development reveals the extent of isoform diversity and potential effects on protein structural changes.Biology open · 2024Article
- AIUPred: combining energy estimation with deep learning for the enhanced prediction of protein disorder.Nucleic acids research · 2024Article
- Assessment of Disordered Linker Predictions in the CAID2 Experiment.Biomolecules · 2024Article
- DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options.Nucleic acids research · 2024Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We expand studies of AlphaFold2 (AF2) in the context of intrinsic disorder prediction by comparing it against a broad selection of 20 accurate, popular and recently released disorder predictors. We use 25% larger benchmark dataset with 646 proteins and cover protein-level predictions of disorder content and fully disordered proteins. AF2-based disorder predictions secure a relatively high Area Under receiver operating characteristic Curve (AUC) of 0.77 and are statistically outperformed by several modern disorder predictors that secure AUCs around 0.8 with median runtime of about 20 s compared to 1200 s for AF2. Moreover, AF2 provides modestly accurate predictions of fully disordered proteins (F1 = 0.59 vs. 0.91 for the best disorder predictor) and disorder content (mean absolute error of 0.21 vs. 0.15). AF2 also generates statistically more accurate disorder predictions for about 20% of proteins that have relatively short sequences and a few disordered regions that tend to be located at the sequence termini, and which are absent of disordered protein-binding regions. Interestingly, AF2 and the most accurate disorder predictors rely on deep neural networks, suggesting that these models are useful for protein structure and disorder predictions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.