> ## Documentation Index
> Fetch the complete documentation index at: https://docs.tamarind.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# RFdiffusion

> General-purpose protein design

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](https://github.com/RosettaCommons/RFdiffusion)

## Binder Design

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

### 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")

### 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)

## 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.

### 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

### 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)

## 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.

### 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

### 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)

## 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)

### 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")

### 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)

[Try RFdiffusion](https://app.tamarind.bio/tools/rfdiffusion)