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EnzSub embedding archive
This directory stages the precomputed representations used by the EnzSub downstream and analysis workflows. The files are copied from the original experiment directories; the sources remain unchanged.
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ec/: EC classification embeddings for ProtBERT-BFD, ESM-2 650M, and ESM-2 3B. Each backbone includesbase,cpt,base_sub, andcpt_sub.esp/: enzyme embeddings used by the enzyme-substrate specificity task.as/: per-residue embeddings used by active-site prediction.pH/andtm/: sequence-level embeddings used by the two regression tasks.transfer/ReactZyme/: the four models in the main ReactZyme configuration, together with the MAT reaction embeddings required by that workflow.transfer/Seq2Topt/: precomputed per-sequence feature caches.transfer/UniKP/: EnzSub/UniKP feature matrices and sequence caches for the kcat, Km, and joint kcat/Km comparisons.rns/: base and CPT representations plus metadata for Random Neighbor Score analysis.
HCFT reuses the EC embeddings, and substrate-neighborhood coherence reuses the ESP embeddings; these representations are not duplicated. CLEAN artifacts are not included.
The pre-existing as/0.4B/protbert_bfd_* checkpoint-selection directories are
legacy selection artifacts, not part of the four-state main comparison. They
have been retained because this organization pass was copy-only.
No project-level data license is granted by this staging directory. Add the chosen data license and repository record before public release.
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