bioemu

name: bioemu description: Generate and analyze protein conformational ensembles using BioEmu. license: MIT

Activation Conditions

Activate when users ask about BioEmu sampling, protein conformational ensembles, equilibrium structures, cryptic pockets, or protein dynamics analysis.

Scope Boundaries

• Focus on setup, inference routing, and output interpretation guidance.
• Enforce credential safety rules and avoid exposing secrets.

Quick Context

• Reference app backend: assets/reference-app/server.
• Reference app frontend: assets/reference-app.
• Backend and frontend installs may each take several minutes on first run.
• Configure credentials in .env without exposing secret values.

Included Capabilities

• Ensemble generation and conformational sampling.
• Azure-backed inference integration.
• MDTraj-based trajectory analysis.
• Optional assistant-style workflows.

Workflow

1. Confirm credentials are configured in .env without requesting secret values.
2. Route setup and first-run execution to docs/quick-start.md.
3. Route model behavior and limitations to docs/model-details.md.
4. Route data formats and integration to docs/data-integration.md.
5. Route errors to docs/troubleshooting.md.

Routing

• docs/quick-start.md for reference app startup.
• docs/application-patterns.md for usage examples.
• docs/azure-setup.md for Azure deployment.
• docs/model-details.md for capability and limitation questions.

Additional Resources

• Blog overview: https://www.microsoft.com/en-us/research/blog/exploring-the-structural-changes-driving-protein-function-with-bioemu-1/
• Video overview: https://www.microsoft.com/en-us/research/video/scalable-emulation-of-protein-equilibrium-ensembles-with-bioemu/
• Technical deep dive: https://www.microsoft.com/en-us/research/video/scalable-emulation-of-protein-equilibrium-ensembles-with-bioemu-2/

Reference Links

• BioEmu on GitHub: https://github.com/microsoft/bioemu
• BioEmu on Azure AI Foundry: https://ai.azure.com/explore/models/BioEmu