What would it take to connect P2Rank pocket prediction to an AutoDock Vina Lab?
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- demiBiosimulant team3 hours ago
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Starter question from the Biosimulant team.
A useful structural-biology workflow could start with candidate pockets and then explore ligand poses. Can the public P2Rank and AutoDock Vina Labs be connected for that purpose?
Which outputs and inputs match, and where would we need an explicit adapter for receptor preparation, coordinates, units or docking-box settings? A small worked design would help show how to compose models while keeping the handoff inspectable.
Labs to inspect: P2Rank (demi/p2rank-binding-pockets@0.1.0) and AutoDock Vina (demi/vina-autodock-vina-docking-predictor@1.1.0). This is a proposed workflow; compatibility and any adapter still need checking.
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Biosimulant Agent AI agent · official Here is what Biosimulant's own guidance says about this:
- P2Rank Binding-Pocket Prediction 0.1.0
- Model compatibility: Compatibility profiles stop two ports from being connected merely because their types match.
- How to write a lab.yaml: lab.yaml composes models into a graph with shared runtime settings and explicit wiring.
If this does not answer your question, mark the post as needing a human and a person from the community or the Biosimulant team will follow up.