ESMFold

Pick ESMFold when you need the fastest possible monomer fold. No MSA, no multimer, single-sequence ESM-2 language-model prediction. Pair with ColabFold (D3) for multimers or AF2 standalone (D2) for full MSA-backed accuracy.

ESMFold (Lin et al., Science 2023). Single-sequence monomer structure prediction from the ESM-2 language model. No MSA, no multimer support. Fastest fold available when an MSA is unavailable or unhelpful.

When it fits:

• You need a monomer fold in well under a minute.
• Your sequence has no detectable homologs (orphan or designed).
• You're triaging a large set of sequences and need throughput.

You will need:

• Single FASTA sequence (monomer only).
• Sequence length under ~600 residues for best accuracy.

Each run uses a preset that sets the scale and scope:

Standalone with your FASTA

Paste a single-chain FASTA (10 to 400 aa monomer) and get pLDDT plus predicted structure. ~30 s on A100-40GB once the 3B model is warm. No MSA, no multimer. Pair with ColabFold (D3) or AF2 (D2) when you need those.

Batch for many monomers

Fold many monomer sequences (FASTA records or one per line) in a single job, up to 500 records. Each fold is shipped back through the partial-results contract; the results table renders per-design pLDDT, PDB download and NGL viewer as folds complete. Cost scales linearly with batch size.

Predicted PDB with per-residue pLDDT. No PAE (single-sequence prediction has no inter-domain signal). Use as a fast self-consistency check on designed sequences.

Where a tool reports them, the scores mean:

ipTM

Predicted confidence in the binder to target interface. Higher is better. Aim above roughly 0.7 on a tractable target.

pLDDT

Per-residue confidence in the predicted fold. Higher means the model is more sure of that part of the structure.

i_pAE and pAE

Predicted alignment error, at the interface (i_pAE) or across the whole structure (pAE). Lower is better.

Lin et al., Science 2023