plip-interaction-analysis

name	plip-interaction-analysis
description	Profile noncovalent protein-ligand interactions with a pinned PLIP release and compare interaction fingerprints across experimental structures, docking poses, or trajectory representatives. Use after structure preparation or pose generation.
license	MIT

PLIP Interaction Analysis

Workflow

1. Follow $cx-compute-environment; ask once before installing pinned PLIP/Open Babel dependencies or processing many structures.
2. Record structure source, assembly/chains, ligand identifier and atom mapping, protonation, waters/metals retained, and whether the pose is experimental, predicted, docked, or an MD frame.
3. Smoke-test one complex. Run PLIP into artifacts/<run-id>/plip/, preserving machine-readable output and exact command/version.
4. Report hydrogen bonds, hydrophobic contacts, salt bridges, pi interactions, halogen bonds, water bridges, and metal coordination with residue/atom IDs and geometry. Compare fingerprints only after consistent preparation.
5. For trajectories, cluster or sample prespecified frames and report interaction occupancy with autocorrelation-aware uncertainty; do not treat every frame as independent.

Boundaries

• A detected contact is a geometry-based annotation, not proof of energetic importance or binding.
• Protonation, missing hydrogens, alternate locations, and water handling can change the fingerprint; state them.
• Do not infer affinity from interaction counts.