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cytokineking/FreeBindCraft

A fork of BindCraft for protein binder design that makes PyRosetta optional, replacing its relaxation and scoring steps with open-source tools.

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What is it?

FreeBindCraft is a modified version of BindCraft, a pipeline for designing protein binders such as miniproteins and peptides against a target structure. The fork adds a --no-pyrosetta flag that lets the pipeline run without a PyRosetta license, which is useful when commercial licensing is a barrier.

In bypass mode, structural relaxation uses an OpenMM-based protocol with PDBFixer preparation and optional GPU acceleration, followed by FASPR side-chain repacking. Shape complementarity is computed with the open-source sc-rs library, and solvent accessible surface area with FreeSASA or a Biopython fallback. Some Rosetta-only metrics have no open-source equivalent and are replaced with placeholder values, so filter results should be interpreted with care.

The fork also adds ipSAE scoring, an interface quality metric based on AlphaFold PAE, and offers an option to rank final designs by it. It includes an interactive setup wizard, a Docker build with an interactive wrapper, and an Apple Silicon path marked experimental.

Key features

  • 01Runs BindCraft without a PyRosetta license via the --no-pyrosetta flag.
  • 02Relaxes structures with an OpenMM protocol that can use CUDA GPUs, followed by FASPR side-chain repacking.
  • 03Computes shape complementarity with sc-rs and SASA with FreeSASA or Biopython.
  • 04Adds ipSAE scoring and an option to rank final designs by it.
  • 05Provides an interactive setup wizard and a Docker wrapper for configuration and runs.

Use cases

  • Designing protein binders on a Linux GPU workstation where a PyRosetta license is unavailable or undesirable.
  • Comparing open-source and PyRosetta-based interface metrics on a folder of structures.
  • Ranking binder designs by ipSAE instead of the default i_pTM.

Quick start

  1. 1

    Clone the repository

    git clone https://github.com/cytokineking/FreeBindCraft [install_folder]
  2. 2

    Run the installer without PyRosetta (Linux x86_64 with NVIDIA driver 575.57.08 or newer)

    bash install_bindcraft.sh --no-pyrosetta
  3. 3

    Activate the Conda environment

    conda activate BindCraft
  4. 4

    Run BindCraft in bypass mode with your target settings

    python -u ./bindcraft.py --settings './settings_target/your_target.json' --filters './settings_filters/default_filters.json' --advanced './settings_advanced/default_4stage_multimer.json' --no-pyrosetta

Things to know

  • Requires Linux x86_64 with an NVIDIA GPU and driver 575.57.08 or newer for the tested installation.
  • Rosetta-specific metrics without open-source equivalents are not computed and use placeholder values.
  • The license is listed as NOASSERTION, so check the repository's license terms before use.

Topics

#protein-design#bindcraft#peptide-design#protein-binder#openmm#structural-biology#bioinformatics#miniprotein#open-source#peptide

FAQ

What is FreeBindCraft?
A fork of BindCraft for protein binder design that makes PyRosetta optional, replacing its relaxation and scoring steps with open-source tools. FreeBindCraft is a modified version of BindCraft, a pipeline for designing protein binders such as miniproteins and peptides against a target structure. The fork adds a --no-pyrosetta flag that lets the pipeline run without a PyRosetta license, which is useful when commercial licensing is a barrier.
Is FreeBindCraft free to use? What license does it have?
FreeBindCraft is open source under the Other license. Check the license terms before using it in commercial products.
Is FreeBindCraft still maintained?
Actively maintained. The last commit to FreeBindCraft was on Oct 20, 2026.
What can I use FreeBindCraft for?
Designing protein binders on a Linux GPU workstation where a PyRosetta license is unavailable or undesirable. Comparing open-source and PyRosetta-based interface metrics on a folder of structures. Ranking binder designs by ipSAE instead of the default i_pTM.
How do I install FreeBindCraft?
Clone the repository: git clone https://github.com/cytokineking/FreeBindCraft [install_folder] Run the installer without PyRosetta (Linux x86_64 with NVIDIA driver 575.57.08 or newer): bash install_bindcraft.sh --no-pyrosetta Activate the Conda environment: conda activate BindCraft Run BindCraft in bypass mode with your target settings: python -u ./bindcraft.py --settings './settings_target/your_target.json' --filters './settings_filters/default_filters.json' --advanced './settings_advanced/default_4stage_multimer.json' --no-pyrosetta
Where can I get FreeBindCraft?
The source code and installation instructions are on GitHub: https://github.com/cytokineking/FreeBindCraft

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