AlphaFold2: A Role for Disordered Protein/Region Prediction?
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Abstract
The development of AlphaFold2 marked a paradigm-shift in the structural biology community. Herein, we assess the ability of AlphaFold2 to predict disordered regions against traditional sequence-based disorder predictors. We find that AlphaFold2 performs well at discriminating disordered regions, but also note that the disorder predictor one constructs from an AlphaFold2 structure determines accuracy. In particular, a naïve, but non-trivial assumption that residues assigned to helices, strands, and H-bond stabilized turns are likely ordered and all other residues are disordered results in a dramatic overestimation in disorder; conversely, the predicted local distance difference test (pLDDT) provides an excellent measure of residue-wise disorder. Furthermore, by employing molecular dynamics (MD) simulations, we note an interesting relationship between the pLDDT and secondary structure, that may explain our observations and suggests a broader application of the pLDDT for characterizing the local dynamics of intrinsically disordered proteins and regions (IDPs/IDRs).
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Preliminary studies suggest most targets with very low pLDDT (<50) are likely IDPs/IDRs rather than well-folded proteins AF2 fails to predict.
“Preliminary studies suggest that the majority of targets with very low-confidence score (pLDDT < 50) assigned by AF2 are likely to be IDPs / IDRs rather than well-folded structures that AF2 fails to predict42–44”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [43]
Previous deep learning models usually sample a sub-sequence with fixed length.
“Previous deep learning models usually sample a sub-sequence with fixed length (20).”
From High-resolution <i>de novo</i> structure prediction from primary sequence (2022) · cites this paper as [20]
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Self-citationAlphaFold: A Special Issue and A Special Time for Protein Science
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Matrin3: Disorder and ALS Pathogenesis
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Assessment of Disordered Linker Predictions in the CAID2 Experiment
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The regulatory functions of ESX-1 substrates, EspE and EspF, are separable from secretion
Prest, R. J., Korotkov, K. V., & Champion, P. A. (2024) · Journal of Bacteriology · doi:10.1128/jb.00271-24 · Cited by 4 · see citing works
Zheng, S. (2025) · PLOS ONE · doi:10.1371/journal.pone.0313812 · Cited by 4 · see citing works
Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them
Russell, S. L., Penunuri, G., & Condon, C. (2024) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2024.07.001 · Cited by 3 · see citing works
Survey of the Aβ-peptide structural diversity: molecular dynamics approaches
Tolstova, A. P., Adzhubei, A. A., Strelkova, M. A., Makarov, A. А., & Mitkevich, V. A. (2024) · Biophysical Reviews · doi:10.1007/s12551-024-01253-y · Cited by 4 · see citing works
- Authors
- Wilson, C. J., Choy, W.-Y., & Karttunen, M.
- Affiliations
- Western University (CA)
- Corresponding author
- Karttunen, Mikko
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2022-04-21
- Volume
- 23
- Issue
- 9
- Pages
- 4591
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC9104326
- OpenAlex
- W4224259818
- Cited by
- 173
- References
- 102
- Citations by year
- 2026: 32 · 2025: 35 · 2024: 39 · 2023: 48 · 2022: 18 · 2012: 1
- FWCI
- 11.51
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Compute Canada
- Canada Research Chairs
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- AlphaFold2, intrinsically disordered proteins, intrinsically disordered regions, disorder prediction, pLDDT, secondary structure, protein structure prediction, molecular dynamics simulation, protein dynamics
- MeSH terms
- Protein Domains, Protein Conformation, Protein Structure, Secondary, Molecular Dynamics Simulation, Intrinsically Disordered Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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