Score Binding Pocket Geometry
score_binding_pocket_geometryIdentify and score putative binding pockets in AlphaFold structures using geometry-based heuristics, evaluating druggability and pocket geometry metrics.
Instructions
Identify and score putative binding pockets from AlphaFold geometry.
Detects pockets with a geometry-only heuristic. Residues in the
inner 60 percent of the structure by distance from the centroid are
taken as the pocket-forming core, then grown greedily into clusters
within an 8 Angstrom radius. A cluster is kept as a putative pocket
when it has at least min_pocket_residues members and a mean pLDDT
of at least 50.
Each pocket reports a radius of gyration (compactness of the pocket residues), a centroid offset (distance of the pocket centroid from the structure centroid; larger means more peripheral — a solvent-accessible cleft rather than a dead-central cavity, and NOT a measure of solvent burial), a mean pLDDT, and a druggability index. The druggability index runs 0 to 100 and is the sum of four equally weighted 0 to 25 sub-scores: residue count, radius of gyration, mean pLDDT, and centroid offset.
This is a fast, dependency-free pre-screen, not a substitute for a validated pocket detector such as fpocket or P2Rank. It needs no ML model, is fully reproducible from AlphaFold coordinates, and runs in air-gapped deployments.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| params | Yes |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||