Sep 2026· Zenodo (CERN European Organization for Nuclear Research)
Abstract
Lacuna discovers cryptic binding pockets: sites that are absent or too small to detect in a protein's unbound structure and open only during conformational fluctuation. It generates a conformational ensemble from any input structure, detects pockets independently in every conformer, clusters the detections into persistent sites, and ranks them with a model fitted on within-structure pairs. Ensemble generation is pluggable: normal mode analysis by default, with implicit-solvent molecular dynamics, Boltz-2 diffusion sampling, or a user-supplied ensemble as alternatives. On the designated CryptoBench test fold it recovers 55.6% of cryptic sites in its top five, rising to 66.1% with an optional PLM-assisted ranker, and 73%, 45% and 87% on the PocketMiner set, a curated set of literature apo/holo pairs, and COACH420 respectively. The default backend completes in a median of 2.6 seconds per chain on one CPU core. Outputs are docking-ready Boltz YAML constraints, AutoDock Vina boxes and pseudoatom PDB files.
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