Boltz-2 Structure Refinement

Refines protein structures using Boltz-2 with inference-time potentials for improved accuracy and quality.

Quick Start

1. Provide a PDB structure as input.
2. Set the desired random seed and optional refinement parameters.
3. Run the node to generate refined structures and confidence scores.

Setup Guide

1. Prepare Input

1. Obtain or generate a PDB structure to refine.
2. Ensure the structure is in the correct PDB dictionary format.

2. Configure Node

1. Set the seed for reproducibility (integer).
2. Optionally adjust recycling steps, number of samples, and potentials usage.

3. Run Refinement

1. Execute the node to receive refined structures and confidence metrics.

Basic Usage

Refining a Predicted Structure

• Use after initial structure prediction to improve model quality.
• Supports batch refinement by increasing diffusion_samples.
• Recommended to keep use_potentials enabled for best results.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Input PDB structure to refine	PDB	{"design_0": "...PDB content..."}
seed	Random seed for reproducibility	INT	42

Optional Inputs

Field	Description	Type	Example
recycling_steps	Number of recycling iterations (higher = better quality)	INT	3
diffusion_samples	Number of refined structures to generate	INT	3
use_potentials	Use inference-time potentials (recommended)	BOOLEAN	True
output_format	Output file format	COMBO ("pdb", "mmcif")	"pdb"

Outputs

Field	Description	Type	Example
refined_structures.pdb	Refined structure(s) as a dict	PDB	{"design_0_ranked_0": "...PDB..."}
confidence.json	Confidence scores for each refined structure	JSON	{"design_0_ranked_0": 0.92}

Best Practices

Refinement Settings

• Enable use_potentials for improved physical plausibility.
• Increase recycling_steps for higher accuracy if runtime allows.

Batch Processing

• Use higher diffusion_samples to explore multiple refined conformations.
• Review confidence scores to select the best refined model.

Troubleshooting

Common Issues

• Input format error: Ensure the PDB input is a dictionary with valid PDB content.
• No output generated: Check that all required fields are provided and input is not empty.

Need Help?

• Contact support for further assistance.