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Boltz-2 Complex Molecular Assembly

Boltz-2 Complex Molecular Assembly enables the joint prediction and assembly of multi-component biomolecular complexes, including proteins, DNA, RNA, and ligands, with optional constraints and affinity prediction.

Boltz-2 Complex Molecular Assembly

Quick Start

  1. Prepare FASTA sequences for each molecular component (protein, DNA, RNA) as needed.
  2. (Optional) Provide ligand SMILES or CCD codes, and custom MSAs for proteins.
  3. (Optional) Specify binding or contact constraints.
  4. Set prediction parameters (e.g., recycling steps, diffusion samples).
  5. Run the node to generate assembled complex structures and confidence/affinity scores.

Setup Guide

1. Prepare Molecular Inputs

  1. Collect and format protein, DNA, RNA sequences in FASTA format.
  2. List ligand SMILES or CCD codes (one per line).
  3. (Optional) Prepare A3M MSAs for proteins.

2. Configure Assembly and Constraints

  1. (Optional) Define binding or contact constraints as described in the node UI.
  2. (Optional) Enable affinity prediction and specify binder chain if needed.
  3. Adjust prediction parameters (recycling steps, diffusion samples, etc.).

Basic Usage

Multi-Component Assembly

  • Assemble complexes from any combination of proteins, DNA, RNA, and ligands.
  • Optionally provide MSAs for improved protein modeling.
  • Apply binding/contact constraints to guide assembly.
  • Predict binding affinity for ligand-containing complexes.

Configuration

Required Inputs

Field Description Type Example
seed Random seed for reproducibility INT 42

Optional Inputs

Field Description Type Example
protein_sequences Protein sequences in FASTA format FASTA >A\nMKVL...\n>B\nGYLL...
dna_sequences DNA sequences in FASTA format FASTA >DNA1\nATCG...
rna_sequences RNA sequences in FASTA format FASTA >RNA1\nAUCGA...
ligand_smiles Ligand SMILES strings (one per line) STRING CCO\nCC(=O)O
ligand_ccd_codes Ligand CCD codes (one per line) STRING ATP\nGTP
protein_msas Custom MSAs for proteins A3M {"A": "..."}
binding_constraints Binding constraints (see UI) STRING A:B:10,20
contact_constraints Contact constraints (see UI) STRING A:10-B:20
predict_affinity Enable binding affinity prediction BOOLEAN True
affinity_binder_chain Chain ID for affinity calculation STRING L1
recycling_steps Number of recycling iterations INT 3
diffusion_samples Number of structure samples INT 1
use_potentials Use potentials for improved accuracy BOOLEAN False
output_format Output file format COMBO pdb

Outputs

Field Description Example
structures.pdb Assembled complex structures (ranked) {"A": "...PDB..."}
confidence.json Confidence scores for predictions {"A": 0.92}
affinity.json Binding affinity scores (if enabled) {"A": -7.5}

Best Practices

Input Preparation

  • Provide high-quality, correctly formatted FASTA sequences for all components.
  • Supply MSAs for proteins when possible to improve structure accuracy.

Constraints & Affinity

  • Use binding/contact constraints to guide specific interactions.
  • Enable affinity prediction only when ligands are present and specify the correct binder chain.

Troubleshooting

Common Issues

  • Missing molecular components: At least one protein, DNA, RNA, or ligand must be provided.
  • MSA not provided: Results may be lower quality for proteins without MSAs.
  • Affinity prediction error: Ensure at least one ligand is present and binder chain is specified or auto-detectable.

Need Help?

  • Contact support for further assistance.