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Does the HuggingFace checkpoint biohub/ESMFold2-Experimental-Fast correspond to the model the ESMFold2 paper calls ESMFold2-Experimental-Fast-cutoff2021? #411
Description
The paper appendix describes a protein binder design protocol that ranks designs with a four-model ensemble, which A.3.2.1 names as:
- ESMFold2-Experimental-Fast-cutoff2021
- ESMFold2-Experimental-Fast-cutoff2025
- ESMFold2-Experimental-cutoff2021
- ESMFold2-Experimental-cutoff2025
A different appendix section A.2.12 lists the same checkpoints for the same roles but names two of them without any cutoff suffix:
- ESMFold2-Experimental
- ESMFold2-Experimental-cutoff2025
- ESMFold2-Experimental-Fast
- ESMFold2-Experimental-Fast-cutoff2025
On HuggingFace there are four repos:
- ESMFold2-Experimental
- ESMFold2-Experimental-Fast
- ESMFold2-Experimental-Cutoff2025
- ESMFold2-Experimental-Fast-Cutoff2025
No mention of 2021 cutoff. The apparent implication is that the plain-named repos are the cutoff2021 models, but nowhere is this stated, which is ambiguous. So my question is,
Does the HuggingFace checkpoint
biohub/ESMFold2-Experimental-Fastcorrespond to the model the ESMFold2 paper calls ESMFold2-Experimental-Fast-cutoff2021?
If so, this should be clarified somewhere, for example in the github README and the huggingface model cards.
Activity
faustomilletari commentedon Sep 22, 2026
Yes.
biohub/ESMFold2-Experimental-Fast is the model the paper calls ESMFold2-Experimental-Fast-cutoff2021, and biohub/ESMFold2-Experimental is ESMFold2-Experimental-cutoff2021.
Both were trained with a PDB release-date cutoff of 2021-09-30. There are four checkpoints in total, not eight — appendix A.2.12's naming matches what is published; A.3.2.1 states the 2021 cutoff explicitly for the same two models.
You are right that this is not documented anywhere public, and we will add the cutoff date to the four model cards and the README.