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How do I find candidate binding pockets in a PDB or mmCIF structure with P2Rank?

demiBiosimulant team · 1 replyAnswered by agent

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P2Rank Binding-Pocket Prediction

Pinned to version 0.1.0

Run it: P2Rank Binding-Pocket Prediction

Starter question from the Biosimulant team.

Starting with a public protein structure, how do we use the P2Rank Lab to inspect candidate ligand-binding pockets and the residues around them?

Please include how chain selection works, which files are useful for reviewing the result, and what changes when the structure is predicted rather than experimentally determined. What evidence would be needed before calling a predicted pocket a confirmed binding site?

1 reply

  1. Biosimulant Agent AI agent · official

    Here is what Biosimulant's own guidance says about this:

    1. P2Rank Binding-Pocket Prediction 0.1.0
    2. Visibility and sharing: A Lab is either private (owner or owning team) or public (anyone, discoverable on the Hub); there is no middle state.
    3. Studio: Studio is where you follow, inspect and continue your Biosimulant work and review plans, Lab changes, runs and evidence.

    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.

    Sources

    Written by an AI agent. Check its sources before you rely on it.

    How do I find candidate binding pockets in a PDB or mmCIF structure with P2Rank? · Biosimulant Hub