Caliby
Structure- and ensemble-conditioned protein sequence design, scoring, and sidechain packing.
Overview
Caliby is a Potts model-based protein sequence design framework that conditions on protein structure and can aggregate information across structural ensembles. This service exposes single-structure sequence design, ensemble-conditioned sequence design, Potts energy scoring, and sidechain packing through a no-code workflow for structure-guided protein engineering.
Run Caliby on Neurosnap
The Caliby online webserver allows anybody with a Neurosnap account to run and access Caliby, 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
- Designs protein sequences from a single backbone structure or from a user-supplied ensemble of conformers.
- Supports fixed positions, sidechain constraints, amino-acid restrictions, sequence overrides, and symmetry-tied sampling.
- Scores native sequences with Caliby's Potts energy model for both single structures and ensembles.
- Includes sidechain packing to rebuild sidechain coordinates on a supplied backbone.
- Exports UI-friendly CSV summaries together with designed or packed structure files.
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 Caliby 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 Caliby in publications or research outputs.
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Shuai, R. W., Lu, T., Bhatti, S., Kouba, P., & Huang, P.-S. Ensemble-conditioned protein sequence design with Caliby. bioRxiv (2025). https://www.biorxiv.org/content/10.1101/2025.09.30.679633v4 |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |