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 Installation Guide to set up Modal and biomodals.

Option 1: Modal (recommended)

cd biomodals
modal run modal_bindcraft.py \
  --target-pdb target.pdb \
  --target-chain A \
  --binder-lengths 70-100 \
  --hotspots "A45,A67,A89" \
  --num-designs 50

GPU: L40S (48GB) | Timeout: 3600s default

Option 2: Local installation

git clone https://github.com/martinpacesa/BindCraft.git
cd BindCraft
pip install -r requirements.txt

python bindcraft.py \
  --target target.pdb \
  --target_chains A \
  --binder_lengths 70-100 \
  --hotspots A45,A67,A89 \
  --num_designs 50

Key parameters

Parameter	Default	Range	Description
--target-pdb	required	path	Target structure
--target-chain	required	A-Z	Target chain(s)
--binder-lengths	70-100	40-150	Length range
--hotspots	None	residues	Target hotspots
--num-designs	50	1-500	Number of designs
--protocol	default	fast/default/slow	Quality vs speed

Protocols