boltz

name	boltz
description	Structure prediction using Boltz-1/Boltz-2, an open biomolecular structure predictor. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-qc. For AlphaFold2 prediction, use alphafold. For Chai prediction, use chai.
license	MIT
category	design-tools
tags	["structure-prediction","validation","open-source"]
source	https://github.com/adaptyvbio/protein-design-skills

Boltz Structure Prediction

Prerequisites

Requirement	Minimum	Recommended
Python	3.10+	3.11
CUDA	12.0+	12.1+
GPU VRAM	24GB	48GB (L40S)
RAM	32GB	64GB

How to run

Option 1: Modal

cd biomodals
modal run modal_boltz.py \
  --input-faa complex.fasta \
  --out-dir predictions/

Option 2: Local

pip install boltz
boltz predict --fasta complex.fasta --output predictions/

Output format

predictions/
├── model_0.cif       # Best model (CIF format)
├── confidence.json   # pLDDT, pTM, ipTM
└── pae.npy

Comparison

Feature	Boltz-1	Boltz-2	AF2-Multimer
MSA-free	Yes	Yes	No
Open source	Yes	Yes	Yes
Speed	Fast	2x faster	Slower

Typical performance

Campaign	Time (L40S)	Cost (Modal)
100 complexes	30-45 min	~$8
500 complexes	2-3h	~$35

Troubleshooting

Error	Cause	Fix
CUDA out of memory	Complex too large	Use --use_msa_server false
KeyError: 'iptm'	Single chain	Ensure 2+ chains in FASTA
FileNotFoundError: weights	Missing model	Run boltz download first

Next: protein-qc for filtering and ranking.