bindcraft

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

# BindCraft is configured with JSON files, not flags
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