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ESMFold is a folding oracle that wraps Meta’s ESMFold model for single-sequence protein structure prediction. It returns 3D atomic coordinates along with confidence metrics (pLDDT, pTM, PAE) that are consumed by structure-based energy terms. For multimer prediction, ESMFold uses either a glycine linker between chains or a gap in positional embeddings (default: skip of 512) to signal chain boundaries. These can be configured via the config parameter.
ESMFold inference is powered by boileroom. boileroom handles model loading, GPU execution, and dependency isolation — either serverlessly via Modal or locally via Apptainer. See the boileroom ESMFold reference for backend configuration details.

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Parameters

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use_modal
bool
default:"False"
Whether to run ESMFold on Modal’s serverless GPU infrastructure. Set to True for serverless execution (no local GPU required), or False for local GPU execution.
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config
dict[str, Any]
default:"{}"
Model-specific configuration. Common keys:
  • glycine_linker (str): linker sequence between chains (e.g., "GGGG"). Default: no linker.
  • position_ids_skip (int): gap in positional embeddings between chains. Default: 512.
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modal_app_context
App | None
default:"None"
Optional Modal app context for reusing an existing Modal session.

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Attributes

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result_class
Type[ESMFoldResult]
The result class for this oracle. ESMFoldResult extends FoldingResult with ESMFold-specific attributes (pLDDT, pTM, PAE arrays).

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Methods

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fold

Fold a list of chains using ESMFold. Parameters
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chains
List[Chain]
required
The chains to fold. For multimer prediction, pass multiple chains.

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Example

import bagel as bg

# Create an ESMFold oracle using Modal
esmfold = bg.oracles.ESMFold(use_modal=True, config={
    "glycine_linker": "GGGG",
    "position_ids_skip": 1024,
})

# Use with energy terms
state = bg.State(
    chains=[binder, target],
    energy_terms=[
        bg.energies.PTMEnergy(oracle=esmfold, weight=1.0),
        bg.energies.PLDDTEnergy(oracle=esmfold, weight=1.0, residues=[binder_residues]),
    ],
    name="binding",
)