How to Use AntiFold
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Use AntiFold online for antibody inverse folding and structure-guided sequence redesign.
AntiFold is an inverse-folding model specialized for antibodies, nanobodies, and antibody-antigen complexes. Instead of predicting structure from sequence, it proposes new sequences that remain compatible with a given immune-receptor structure, making it useful for homolog generation, conservative redesign, and antibody optimization.
On Neurosnap, you start from an antibody or complex structure and sample alternative sequences while tracking confidence, sequence recovery, and residue-level amino-acid probabilities. That keeps the workflow anchored to a known binding geometry rather than unconstrained sequence generation.
How AntiFold Works
The method adapts inverse folding to the peculiarities of antibody structure and sequence space, which differ substantially from generic protein backbones. By conditioning on the three-dimensional structure, AntiFold can score or sample variants that preserve fold compatibility while still exploring positions where the model sees room for change.
On Neurosnap, controls such as Number Sequences, Sampling Temperature, and Experiment Seed let users move between conservative and exploratory redesign. The results page emphasizes proposed sequences, confidence and recovery summaries, and position-wise amino-acid probabilities so researchers can rationally choose candidates for expression or binding follow-up.
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 AntiFold on Neurosnap
Using AntiFold on Neurosnap could drastically accelerate antibody inverse folding and structure-guided variant design from antibody or complex structures.
- Study-fit inputs: AntiFold works from antibody, nanobody, or antibody-antigen structures, so redesign stays anchored to the fold and interface you already care about.
- Structure-aware redesign: The method explores sequence space under structural constraints instead of proposing unconstrained sequence edits.
- Protocol control: Researchers can tune
Number Sequences,Sampling Temperature, andExperiment Seedto move between conservative reconstruction and broader sampling. - Readable evidence: Sequence tables, recovery statistics, confidence summaries, and amino-acid probability maps make candidate comparison straightforward.
- Faster iteration: Managed execution on Neurosnap removes infrastructure overhead so teams can focus on antibody design decisions rather than custom inverse-folding workflows.
How to Use AntiFold on Neurosnap
To harness the capabilities of AntiFold, 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 AntiFold.
- Provide Inputs: Provide all the inputs specified within the submission panel and optionally configure the tool as desired.
- Run Tool: Submit the AntiFold 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.
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