The AlphaFold Database of Protein Structures: A Biologist’s Guide
Open accessAbstract
AlphaFold, the deep learning algorithm developed by DeepMind, recently released the three-dimensional models of the whole human proteome to the scientific community. Here we discuss the advantages, limitations and the still unsolved challenges of the AlphaFold models from the perspective of a biologist, who may not be an expert in structural biology.
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PAE values are only confidence estimates, and PAE accuracy for inter-domain prediction has been benchmarked less extensively than for intra-domain contacts.
“it is important to remember that the PAE values are only confidence estimates. Furthermore, the accuracy of PAE graphs for inter-domain prediction has not been as extensively benchmarked as for intra-domain contacts36”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [36]
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The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins
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“Furthermore, the accuracy of PAE graphs for interdomain prediction has not been as extensively benchmarked as for intradomain contacts 36 .”
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- Authors
- David, A., Islam, S., Tankhilevich, E., & Sternberg, M. J. E.
- Affiliations
- Imperial College London (GB)
- Corresponding author
- David, Alessia
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2022-01
- Volume
- 434
- Issue
- 2
- Pages
- 167336
- ISSN
- 0022-2836 (ISSN-L)
- PMC
- PMC8783046
- OpenAlex
- W3208999135
- Cited by
- 268
- References
- 23
- Citations by year
- 2026: 30 · 2025: 43 · 2024: 70 · 2023: 79 · 2022: 45 · 2012: 1
- FWCI
- 15.46
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust
- BBSRC
- 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 › Machine Learning in Bioinformatics
- Keywords
- AlphaFold, protein structure prediction, human proteome, deep learning, protein 3D structure, structural biology
- MeSH terms
- Deep Learning, Algorithms, Humans, Models, Molecular, Molecular Biology, Protein Conformation, Databases, Factual, Protein Folding, Computational Biology, Proteome
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