BindCraft2
Campaign-based protein binder design across multiple binder modalities.
Overview
BindCraft 2.0 is a campaign-based protein binder design suite for de novo miniproteins, scaffolded binders, cyclic peptides, oligomeric binders, antibody-like scaffolds, and multistate objectives. It combines AlphaFold2-guided sequence optimization, ProteinMPNN redesign, validation with held-out AlphaFold models, and structural filters to produce ranked candidate complexes for experimental follow-up.
Run BindCraft2 on Neurosnap
The BindCraft2 online webserver allows anybody with a Neurosnap account to run and access BindCraft2, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Supports de novo binders, larger binders, linear peptides, cyclic peptides, homo-oligomers, multidomain binders, VHHs, ARPs, scFvs, Fabs, and conformational binder design presets.
- Accepts target structures with optional chain, hotspot, and coldspot selections for epitope-focused campaigns.
- Exposes BindCraft 2.0 biological properties such as focused epitope targeting, humanization, protease stability, disulfide staples, topology bias, termini objectives, initial guess, and big bang starts.
- Exports ranked accepted designs, candidate refolding records, trajectory summaries, campaign summaries, and predicted complex structures.
- Uses a streamlined campaign form while keeping target paths, output folders, and runtime-sensitive settings managed by Neurosnap.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access BindCraft2 using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using BindCraft2 in publications or research outputs.
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PacesaLab. BindCraft2: Easy to use suite for designing a wide range of protein binder modalities. https://github.com/PacesaLab/BindCraft2 |
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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 |
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Jumper et al. "Highly accurate protein structure prediction with AlphaFold." Nature (2021) doi: 10.1038/s41586-021-03819-2 |
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Dauparas, J., et al. "Robust deep learning based protein sequence design using ProteinMPNN." Science (2022) doi: 10.1126/science.add2187 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |