pLDDT Values in AlphaFold2 Protein Models Are Unrelated to Globular Protein Local Flexibility
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Two non-redundant, high-quality sets of protein X-ray crystal structures from the Protein Data Bank (room temperature, 288–298 K, and low temperature, 95–105 K) were compared to structural predictions conducted using ColabFold/AlphaFold2. In particular, the relationship between B-factors and pLDDT values, which estimate the degree of prediction confidence, was investigated. It was observed that there is basically no correlation between these two quantities and, consequently, that the level of confidence in predictions does not provide information about the degree of local structural flexibility of globular proteins.
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Other reports compared pLDDT with crystallographic B-factors and suggested AF2 confidence metrics cannot directly report local flexibility.
“other reports have compared pLDDT scores with crystallographic B-factors to suggest AF2 confidence metrics are unable to provide direct information on local flexibility66”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [66]
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- Authors
- Carugo, O.
- Affiliations
- University of Vienna (AT)
- Corresponding author
- Carugo, Oliviero
- ORCID
- Carugo, Oliviero
- Venue
- Crystals
- Publisher
- MDPI AG
- Published
- 2023-11-01
- Volume
- 13
- Issue
- 11
- Pages
- 1560
- ISSN
- 2073-4352 (ISSN-L)
- OpenAlex
- W4388140476
- Cited by
- 46
- References
- 43
- Citations by year
- 2026: 15 · 2025: 22 · 2024: 9
- FWCI
- 4.09
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Crystals (publishedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Ministero dell’Università e della Ricerca (MUR)
- University of Pavia through the program “Dipartimenti di Eccellenza 2023–2027”
- 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
- pLDDT, AlphaFold2, ColabFold, Debye-Waller factor, protein flexibility, globular proteins, prediction confidence, protein structure prediction, X-ray crystal structure, low-temperature crystal structure
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