Synthyra/ESMFold2-Experimental-Fast-Cutoff2025

FastPLMs ESMFold2

FastPLMs ESMFold2 is a self-contained Hugging Face AutoModel wrapper for Biohub's ESMFold2, ESMFold2-Fast, and experimental ESMFold2 structure predictors. It vendors the released Biohub ESMFold2 model code, input builder, MSA helpers, and structure export utilities, while loading the PLM backbone through FastPLMs ESM++.

Load With AutoModel

import torch
from transformers import AutoModel

model = AutoModel.from_pretrained(
    "Synthyra/ESMFold2-Fast",
    trust_remote_code=True,
    dtype=torch.float32,
).eval().cuda()

Use Synthyra/ESMFold2 for the full model, Synthyra/ESMFold2-Fast for the faster release variant, and the Synthyra/ESMFold2-Experimental* checkpoints for differentiable binder design and experimental critic ensembles. The folding trunk runs in fp32; the 6B FastPLMs ESM++ backbone is loaded in bf16 by default via esmc_precision="bf16" and uses the flex attention backend by default inside ESMFold2.

Fold One Protein

sequence = "MKTLLILAVVAAALA"

result = model.fold_protein(
    sequence,
    num_loops=3,
    num_sampling_steps=50,
    num_diffusion_samples=1,
    seed=0,
)

print(float(result.plddt.mean()))
print(float(result.ptm))

Experimental Test-Time Training

TTT is disabled by default. Standard fold_protein(...), fold(...), raw tensor inference, and state_dict() keys are unchanged unless you explicitly pass ttt=True or call fold_protein_ttt(...).

The ESMFold2 TTT path is experimental and protein-only in v1. It trains local LoRA adapters only on _esmc with a masked language modeling objective. The folding trunk, confidence head, diffusion head, and structure input pipeline are frozen. TTT can improve difficult low-confidence folds, but it adds substantial test-time compute and can degrade already confident predictions.

result = model.fold_protein(
    "MSTNPKPQRKTKRNT",
    num_loops=1,
    num_sampling_steps=10,
    num_diffusion_samples=1,
    seed=0,
    ttt=True,
    ttt_config={
        "steps": 1,
        "ags": 1,
        "batch_size": 1,
        "lora_rank": 8,
        "lora_alpha": 32.0,
    },
)

print(result.ttt_metrics["losses"])
print(result.ttt_metrics["step_plddts"])
print(result.ttt_metrics["best_step"])

load_esmc=True is required for TTT because the ESM++ MLM head is loaded lazily from config.esmc_id. If that pretrained MLM head cannot be loaded, TTT raises an assertion instead of silently using a random head.

Save mmCIF or PDB

model.save_as_cif(result, "prediction.cif")
model.save_as_pdb(result, "prediction.pdb")

cif_text = model.result_to_cif(result)
pdb_text = model.result_to_pdb(result)

result_to_cif preserves the full MolecularComplex. result_to_pdb converts through Biohub's protein-only ProteinComplex representation, so use mmCIF for complexes with ligands or nucleic acids.

Fold Complexes

types = model.input_types

complex_input = types.StructurePredictionInput(
    sequences=[
        types.ProteinInput(id="A", sequence="MKTLLILAVVAAALA"),
        types.DNAInput(id="B", sequence="GATAGC"),
        types.LigandInput(id="L", ccd=["SAH"]),
    ]
)

result = model.fold(
    complex_input,
    num_loops=3,
    num_sampling_steps=50,
    num_diffusion_samples=1,
    seed=0,
)

model.save_as_cif(result, "complex_prediction.cif")

Binder Design With FastPLMs ESMFold2

FastPLMs includes a FastPLMs-only port of the Biohub ESMFold2 binder design tutorial at cookbook/tutorials/binder_design_fastplms.py. The workflow uses ESMFold2 experimental checkpoints for differentiable folding losses, ESM++ for sequence regularization, and ESMFold2 hero critics for final confidence scoring.

The optimizer follows the official strategy:

1. Optimize mutable # residues as continuous amino acid logits.
2. Suppress cysteine design by masking cysteine logits and gradients.
3. Backpropagate through ESMFold2 res_type_soft using intra-contact, inter-contact, and globularity losses from the distogram.
4. Add an ESM++ masked-LM pseudoperplexity regularizer on mutable binder residues.
5. Keep the late-trajectory sequence with the best iPTM.
6. Fold the selected sequence with the final critic ensemble and write results.parquet, selection.parquet, trajectory.jsonl, best_sequences.fasta, and per-critic PDB/CIF/logit files.

Run the verified EGFR 128 amino acid de novo minibinder example:

cd /home/ubuntu/FastPLMs

sudo -n docker run --gpus all --rm \
  -v /home/ubuntu/FastPLMs:/app \
  -v /home/ubuntu/FastPLMs:/workspace \
  -v /home/ubuntu/.cache/huggingface:/workspace/.cache/huggingface \
  -w /workspace fastplms-esmfold2 \
  python /app/cookbook/tutorials/binder_design_fastplms.py \
    --backend local \
    --target-name egfr \
    --binder-sequence '################################################################################################################################' \
    --not-antibody \
    --steps 150 \
    --batch-size 1 \
    --seed 103 \
    --output-dir /workspace/campaign_egfr_len128_b1_s150_seed103_consensus_cli

Verified result:

Metric	Value
Binder length	128
Seed	103
Steps	150
Hero mean iPTM	0.913870
Hero min iPTM	0.904600
All four hero critics above 0.9	True

Binder sequence:

SAVKHLLEIVKYLEEAIEKALEVDPVFLVPPAAEELLIAAKVIKELAKENPELIEVYELLMKAVKGLKKLVRSNDKEILREVIRLLRKAAKVIREILKNNPDLDPELRKALEELAKVLEEIAEVLEQQ

See the full guide in docs/binder_design.md for Modal execution, official pI and selection scoring, per-critic metrics, and the tested cheaper step-count boundary.

Use MSAs

types = model.input_types

msa = types.MSA.from_a3m("query.a3m", max_sequences=128)
input_with_msa = types.StructurePredictionInput(
    sequences=[
        types.ProteinInput(id="A", sequence=msa.query, msa=msa),
    ]
)

result = model.fold(input_with_msa, num_sampling_steps=50, seed=0)

Raw Tensor Inference

features, chain_infos = model.prepare_structure_input(complex_input, seed=0)

with torch.inference_mode():
    output = model(
        **features,
        num_loops=3,
        num_sampling_steps=50,
        num_diffusion_samples=1,
    )

decoded = model.input_builder.decode(output, features, chain_infos)

Set load_esmc=False when loading if you want to provide precomputed lm_hidden_states manually or run folding-trunk tests without loading the 6B ESM++ backbone:

model = AutoModel.from_pretrained(
    "Synthyra/ESMFold2-Fast",
    trust_remote_code=True,
    load_esmc=False,
).cuda().eval()

For FP8 LM inference, install transformer_engine.pytorch in a CUDA environment with FP8-capable hardware and load the shared FastPLMs ESM++ backbone with:

model = AutoModel.from_pretrained(
    "Synthyra/ESMFold2-Fast",
    trust_remote_code=True,
    esmc_precision="fp8",
).cuda().eval()

FP8 is inference-only for the ESMFold2 LM backbone. TTT remains a bf16/fp32 path.