Quartz 4

ESMFold pLDDT weakly correlates with intra-family differences in stability and experimental success, but not differences in cooperativity

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Summary

ESMFold pLDDT correlates with intra-family differences in protein stability and experimental success (expression, monomeric, etc), but not inter-family differences (1,2). Values from other sources AlphaFold2 pLDDT and PAE, and ProteinMPNN likelihoods correlates poorly with expression probability. None of these values consistently correlate with folding cooperativity (e.g., differences in unfolding dynamics).

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Ref (2)

Ref (1)

1.
Ferrari ÁJR, Dixit SM, Thibeault J, Garcia M, Houliston S, Ludwig RW, et al. Large-scale discovery, analysis, and design of protein energy landscapes. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.03.20.644235
2.
Garcia M, Dixit SM, Rocklin GJ. Evaluating zero-shot prediction of protein design success by AlphaFold, ESMFold, and ProteinMPNN. openRxiv; 2025. Available from: https://doi.org/10.1101/2025.07.29.667290

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