Lacuna Cryptic Pocket Discovery

Find cryptic binding pockets in a protein (uploaded or fetched by PDB ID) across a generated conformational ensemble with Lacuna, ranked in an interactive report.

by Temple Compute

Run Lacuna Cryptic Pocket Discovery on Horus

W-33 · Lacuna Cryptic Pocket Discovery

Find cryptic binding pockets in a protein (uploaded or fetched by PDB ID) across a generated conformational ensemble with Lacuna, ranked in an interactive report.

Domain: Drug Discovery

Overview

Finds cryptic binding pockets (sites that open only on ligand binding) with Lacuna. It generates a conformational ensemble from the input structure, detects pockets in every conformer, clusters them across the ensemble and ranks them with a fitted model that also scores crypticity. The example is apo KRAS(G12C), PDB 4LDJ. The workflow has 2 tasks; for docking into the top pocket see W-34.

Pipeline

discover  receptor.pdb or RCSB pdb_id ──► results/pockets/ (pocket_report.json, pocket_*.pdb)
report    pocket_report.json          ──► results/report.html + results/pockets.csv

Inputs / Outputs

Parameters

| id | Default | Meaning | |---|---|---| | receptor | examples/structures/receptor.pdb (4LDJ) | Apo structure, used when pdb_id is empty | | pdb_id | empty | 4-character PDB code to fetch instead of the upload | | conformers | 20 | Ensemble size (5-200) | | detector | surface-fusion | surface-fusion, surface or alpha | | rank_by | learned | learned, crypticity, druggability, balanced or persistence | | top | 10 | Pockets reported (1-50) | | min_druggability | 0 | Drop pockets below this druggability (0-1) |

References