Issues

• can not use ESMFold2-Fast

  Biohub/esm#422 · Filter by author CharlesDDD opened on Oct 5, 2026
  1

• ESMFold2: SMILES ligands are written as LIG, which is a different molecule in the CCD

  Biohub/esm#421 · Filter by author daylight-00 opened on Oct 2, 2026

• ESMFold2: fold() cannot take precomputed LM hidden states

  Biohub/esm#420 · Filter by author daylight-00 opened on Oct 2, 2026

• ESMFold2: a ligand given as several CCD codes is returned as one residue

  Biohub/esm#419 · Filter by author daylight-00 opened on Oct 2, 2026

• ESMFold2: fold(lm_dropout=0) does not turn the LM dropout off

  Biohub/esm#418 · Filter by author daylight-00 opened on Oct 2, 2026

• Does the HuggingFace checkpoint biohub/ESMFold2-Experimental-Fast correspond to the model the ESMFold2 paper calls ESMFold2-Experimental-Fast-cutoff2021?

  Biohub/esm#411 · Filter by author ekiefl opened on Sep 22, 2026
  1

• Questions on design constraints: penalizing multi-residue motifs and suppressing interface beta-sheets

  Biohub/esm#408 · Filter by author Gu-SeongHoe opened on Sep 21, 2026

• Clarification on ESMFold2 training cutoff: deposition date vs. PDB release date, and possible benchmark leakage

  Biohub/esm#406 · Filter by author SanggeunParrk opened on Sep 18, 2026

• Question about the JGI metagenome dataset used for ESMC training

  Biohub/esm#399 · Filter by author kkbiu opened on Sep 5, 2026

• Request to release the designed binder sequences and assay results.

  Biohub/esm#396 · Filter by author JudeWells opened on Sep 3, 2026

• Structure prediction with residue level restraints

  Biohub/esm#336 · Filter by author KejserMikael1 opened on Jun 4, 2026

• Recommended way to assess binding affinities for mAb-antigen predictions?

  Biohub/esm#330 · Filter by author avilella opened on Jun 2, 2026

• Unable to access models through EvolutionaryScale Forge:

  Biohub/esm#296 · Filter by author cgseitz opened on Jan 20, 2026
  3

• Performance discrepancy with nan coordinates vs coordinates=None

  Biohub/esm#294 · Filter by author jsjung00 opened on Dec 19, 2025

• Protein generation around active site without specifying residue numbers

  Biohub/esm#288 · Filter by author Xuebin-Feng opened on Nov 8, 2025

• ESMProtein.from_pdb() ignores HETATOM

  Biohub/esm#287 · Filter by author Ento0n opened on Nov 5, 2025

• Validate ESM3-VQVAE Scripts

  Biohub/esm#277 · Filter by author mahdip72 opened on Oct 3, 2025

• How to enable batch training?

  Biohub/esm#260 · Filter by author yuliangyan0807 opened on Jul 30, 2025
  

• Missing contact-regression model file for esmc_600m_2024_12_v0

  Biohub/esm#259 · Filter by author aowuawu opened on Jul 23, 2025

• ESM models fail on CPU when flash_attn is installed

  Biohub/esm#242 · Filter by author karinazad opened on May 21, 2025

• esm c (esmc-300m-2024-12 or esmc-600m-2024-12): AttributeError: property 'cls_token' of 'EsmSequenceTokenizer' object has no setter.

  Biohub/esm#240 · Filter by author 595693085 opened on May 15, 2025
  3

• How to generate from key words and second structure?

  Biohub/esm#239 · Filter by author MingYangi opened on May 13, 2025

• Code Previously provided

  Biohub/esm#237 · Filter by author grpinto opened on Apr 16, 2025

• Residue annotation always returns zero tensor

  Biohub/esm#236 · Filter by author dandingsky opened on Apr 10, 2025

• chain_id and sequence_id clarification

  Biohub/esm#235 · Filter by author Riccarn opened on Apr 9, 2025