We offer 4 defined tasks to use RFdiffusion: Binder Design, Binder Redesign, Motif Scaffolding, and Partial Diffusion. If you know what you’re doing, you can also specify custom contigs using the format specified by RFdiffusion

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Binder Design

Generate a completely novel binder to a target protein structure, at certain residues known as a “hotspot”.

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Required Parameters

  • PDB File (`pdbFile`): Input PDB file containing the target structure
  • Target Chains (`targetChains`): Chain IDs of the target protein (e.g., [“A”])
  • Binder Length (`binderLength`): Length of the binder region to be designed. Can be a fixed length (e.g., “20”) or a range to sample uniformly (e.g., “20-30”)

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Optional Parameters

  • Hotspots (`binderHotspots`): Specific residues on the target to focus on when designing the binder
  • Number of Designs (`numDesigns`): Number of designs to generate (default: 1)
  • Verify (`verify`): Whether to verify designs with MPNN and AlphaFold (default: true)

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Binder Redesign

Modify parts of an existing protein binder to improve its binding properties or alter ots specificity. This can be useful for optimizing existing protein-protein interactions or adapting binders to new targets.

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Required Parameters

  • PDB File (`pdbFile`): Input PDB file containing the binder/target complex
  • Binder Chain (`binderChain`): Chain ID of the binder chain to be redesigned
  • Designed Residues (`designedResidues`): Residues to be redesigned in the binder chain (format: ranges like “1-5, 7-10”)
  • Designed Lengths (`designedLengths`): Length specifications for each designed region, with lower and upper bounds for sampling

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Optional Parameters

  • Hotspot Chain (`hotspotChain`): Chain to select residues to focus on
  • Hotspots (`hotspots`): Specific residues to focus on during redesign
  • Number of Designs (`numDesigns`): Number of designs to generate (default: 1)
  • Verify (`verify`): Whether to verify designs with MPNN and AlphaFold (default: true)

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Motif Scaffolding

Scaffold existing interface with newly designed regions. This task allows you to preserve important structural or functional elements while generating novel surrounding protein architecture.

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Required Parameters

  • PDB File (`pdbFile`): Input PDB file containing the structure
  • Interface Chain (`interfaceChain`): Chain ID of the chain with interface to be scaffolded
  • Interface Residues (`interfaceResidues`): Residues to be scaffolded (format: ranges like “10-20,30-40”)
  • Designed Lengths (`designedLengths`): Length specifications for each designed region

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Optional Parameters

  • Number of Designs (`numDesigns`): Number of designs to generate (default: 1)
  • Verify (`verify`): Whether to verify designs with MPNN and AlphaFold (default: true)

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Partial Diffusion

Partial diffusion allows you to diversify specific regions of a protein while keeping other parts fixed. This will take into account the initial structure at redesigned residues (as compared to Motif Scaffolding, which will ignore the original residues)

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Required Parameters

  • PDB File (`pdbFile`): Input PDB file containing the structure
  • Designed Chain (`designedChain`): Chain ID of the chain to be designed
  • Diffused Residues (`diffusedResidues`): Residues to be diffused (format: ranges like “1-5, 7-10”)

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Optional Parameters

  • Partial Diffusion Temperature (`partial_T`): Temperature parameter for the diffusion process
  • Number of Designs (`numDesigns`): Number of designs to generate (default: 1)
  • Verify (`verify`): Whether to verify designs with MPNN and AlphaFold (default: true)

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