| name | bindcraft |
| description | End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate.
For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
|
| license | MIT |
| category | design-tools |
| tags | ["structure-design","sequence-design","binder","pipeline"] |
| proteinbase_slug | bindcraft |
| proteinbase_url | https://proteinbase.com/design-methods/bindcraft |
| biomodals_script | modal_bindcraft.py |
BindCraft Binder Design
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| Python | 3.9+ | 3.10 |
| CUDA | 11.7+ | 12.0+ |
| GPU VRAM | 32GB | 48GB (L40S) |
| RAM | 32GB | 64GB |
How to run
First time? See Getting started to set up Modal and biomodals.
Option 1: Modal (recommended)
cd biomodals
modal run modal_bindcraft.py \
--input-pdb target.pdb \
--target-chains A \
--target-hotspot-residues "45,67,89" \
--lengths "70,100" \
--number-of-final-designs 50
GPU: L40S (48GB) | Timeout: 300 min default
Option 2: Local installation
git clone https://github.com/martinpacesa/BindCraft.git
cd BindCraft
python -u ./bindcraft.py \
--settings ./settings_target/mytarget.json \
--filters ./settings_filters/default_filters.json \
--advanced ./settings_advanced/default_4stage_multimer.json
The target PDB, chains, hotspots, and binder length range are set inside the
--settings JSON. See the BindCraft repo for the settings schema.
Key parameters (Modal wrapper)
| Parameter | Default | Description |
|---|
--input-pdb | required | Target structure |
--target-chains | A | Target chain(s) |
--target-hotspot-residues | "" | Target hotspots (e.g. "45,67,89") |
--lengths | 50,130 | Binder length range |
