How to use FreeBindCraft Online

Use FreeBindCraft online for PyRosetta-free de novo protein binder design.

FreeBindCraft is a modified BindCraft workflow that keeps the one-shot binder design loop while adding a PyRosetta bypass. In this Neurosnap service, PyRosetta is not installed or enabled. Relaxation and interface scoring use open-source replacements such as OpenMM, FASPR, FreeSASA, Biopython routines, and sc-rs shape complementarity where available.

Researchers provide a Target Structure, optional Target Chains, optional Hotspots, and binder size bounds. Protocol and filter settings match the familiar BindCraft workflow, while FreeBindCraft-specific controls allow final ranking by either i_pTM or ipSAE.

How FreeBindCraft Works

FreeBindCraft runs the BindCraft-style hallucination, sequence design, prediction, and filtering workflow against a target structure, but it always uses the PyRosetta bypass on Neurosnap. OpenMM handles relaxation, FASPR can repack side chains, FreeSASA or Biopython estimates solvent-accessible surface metrics, and sc-rs provides open-source shape-complementarity scoring when available.

On Neurosnap, Design Protocol, Prediction Protocol, Interface Protocol, Template Protocol, and Filters expose the same core search controls as BindCraft. Ranking Method can keep the default i_pTM ordering or use ipSAE, which focuses on interface predicted structural alignment error. Save Plots and Save Animations control optional visual artifacts without changing the PyRosetta-free execution path.

Results should be read as a ranked design campaign. The CSV summarizes candidate sequences, confidence, interface, relaxation, and scoring metrics, while accepted ranked structures and optional visual artifacts support follow-up triage before expression or validation.

What is Neurosnap?

Neurosnap is the leading platform for bioinformatics and computational science focused on expanding access to powerful modeling and simulation tools. Because many state-of-the-art machine learning systems remain complex to install, configure, and scale, Neurosnap offers a clean, browser-based workspace that removes the burden of infrastructure management, dependency conflicts, and command-line tooling.

Built for biologists, chemists, and cross-disciplinary scientists, the platform enables advanced computational workflows without requiring expertise in software engineering or cloud architecture. Researchers can launch analyses through an intuitive interface, connect programmatically through a comprehensive API, and rely on automated resource management to scale workloads efficiently. By taking care of the underlying compute and operational complexity, Neurosnap allows teams to devote their energy to scientific progress and faster iteration. Security and data protection remain foundational principles, with clear safeguards outlined in our Terms of Use and Privacy Policy to ensure your work stays protected.

Advancing Discovery with FreeBindCraft on Neurosnap

Using FreeBindCraft on Neurosnap could drastically accelerate PyRosetta-free de novo protein binder design with open-source relaxation and interface scoring.

PyRosetta-free execution: Neurosnap forces FreeBindCraft's --no-pyrosetta path and does not install PyRosetta.
Familiar BindCraft controls: Target chains, hotspots, binder lengths, design protocols, filters, and template options carry over for users who already know BindCraft.
Open-source metric path: OpenMM, FASPR, FreeSASA, Biopython, and sc-rs replace Rosetta-dependent relaxation and interface metrics where supported.
Interface-aware ranking: i_pTM and ipSAE ranking options help prioritize candidates by predicted complex quality.

How to Use FreeBindCraft on Neurosnap

To harness the capabilities of FreeBindCraft, researchers can follow this streamlined workflow within Neurosnap:

Access Neurosnap: Start by logging in to the Neurosnap website.
Select Tool: From the list of available tools, choose FreeBindCraft.
Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
Run Tool: Submit the FreeBindCraft job and Neurosnap will execute it in the cloud, automatically notifying you as soon as your results are ready.
Review Output: Explore your results through rich visualizations, including figures, plots, and interactive views designed to help you analyze findings with clarity and confidence.

Citations

Please cite the original work when using FreeBindCraft in publications or research outputs.

Pacesa, M., Nickel, L., Schellhaas, C. et al. One-shot design of functional protein binders with BindCraft. Nature (2025). https://doi.org/10.1038/s41586-025-09429-6

Cytokineking. FreeBindCraft: BindCraft with Optional PyRosetta Bypass. https://github.com/cytokineking/FreeBindCraft

Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189. (doi: 10.12688/f1000research.7931.1)

Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/

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