bindcraft

Automate end-to-end binder design with BindCraft and AF2 validation.

151|20|Updated Jan 15, 2026

Search Tags:#modal #protein design #design campaigns #AF2 validation #BindCraft #binder design

Ready to run

npx skills add https://github.com/adaptyvbio/protein-design-skills --skill bindcraft

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bindcraft
Source: https://github.com/adaptyvbio/protein-design-skills/tree/main/skills/bindcraft
Command: npx skills add https://github.com/adaptyvbio/protein-design-skills --skill bindcraft

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

End-to-end binder design is automated with BindCraft and AF2 validation to accelerate production campaigns and improve design quality.

Core Features & Use Cases

End-to-end binder design and evaluation using BindCraft with integrated AF2 validation.
Supports multiple design protocols (fast, default, slow) and joint backbone/sequence optimization.
Outputs QC metrics and design campaigns suitable for experimental validation.

Quick Start

Example usage: modal run modal_bindcraft.py --target-pdb target.pdb --target-chain A --binder-lengths 70-100 --hotspots A45,A67,A89 --num-designs 50

Frequently Asked Questions about bindcraft

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I automate end-to-end binder design with AF2 validation?▼

End-to-end binder design with AF2 validation is automated by running BindCraft via Modal, requiring a target PDB, chain ID, binder lengths, and hotspot residues to generate evaluated design campaigns.

What inputs do I need for protein binder design and hotspot targeting?▼

Protein binder design and hotspot targeting require a target PDB file, target chain ID, specified binder lengths, and hotspot residues. You also set num_designs and select a design protocol.

Can I run BindCraft on Modal for production protein design campaigns?▼

Yes, BindCraft runs on Modal for production protein design campaigns. Execution requires Python 3.9+ and Modal or biomodals to process the specified target and design parameters.

What is the difference between fast, default, and slow design protocols for binder optimization?▼

Fast, default, and slow design protocols control the speed and depth of joint backbone and sequence optimization during binder design, allowing you to balance throughput against design quality.

How does joint backbone and sequence optimization work in binder design?▼

Joint backbone and sequence optimization in binder design works by simultaneously refining the binder's structural backbone and amino acid sequence to improve binding affinity against specified hotspots.

What outputs and QC metrics does automated binder design generate for experimental validation?▼

Automated binder design generates QC metrics and complete design campaigns evaluated with AF2 validation, providing outputs directly suitable for downstream experimental testing and validation.