Cavity-Guided Virtual Screening

Find the most druggable cavity of a receptor with fpocket, box it, and dock a ligand library into it with AutoDock Vina as a parallel map, ranked by affinity.

by Temple Compute

Run Cavity-Guided Virtual Screening on Horus

W-30 · Cavity-Guided Virtual Screening

Find the most druggable cavity of a receptor with fpocket, box it, and dock a ligand library into it with AutoDock Vina as a parallel map, ranked by affinity.

Domain: BioExcel Building Blocks

Overview

Structure-based virtual screening: fetches a receptor, detects cavities with fpocket, boxes the most druggable one, and docks a ligand library into it with AutoDock Vina, ranked by binding affinity. The docking task is a parallel map with one clone per ligand batch. The workflow has 11 tasks.

Pipeline

fetch_pdb -> extract_protein
fpocket_run -> fpocket_filter -> select_pocket -> fpocket_select -> box   Cavity detection, pocket choice, docking box
str_check_add_hydrogens                                                   Receptor protonation
split_ligands                                                             Split library into batches
dock[00..NN]                                                              AutoDock Vina, one clone per batch
rank                                                                      Rank by affinity, write top poses

Inputs / Outputs

Outputs (results/):

A ligand that fails to dock is recorded in status.json and the summary; it does not fail the task.

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 3HEC | Receptor PDB code; leave empty to use structure. | | structure | examples/3hec.pdb | Receptor PDB file used when pdb_id is empty. | | ligand_library | examples/ligands.sdf | Ligands to screen, SDF or SMILES (.smi). | | rank_by | druggability_score | fpocket metric used to pick the cavity (druggability_score, score, volume). | | residue_selection | empty | MDAnalysis selection of a known site (e.g. resid 71 or resid 104); only cavities within 10 Šof its centre of mass can be picked. Empty considers every filtered cavity. | | min_druggability | 0 | Cavities with a lower fpocket druggability score are dropped (0-1); fpocket score window is fixed at [0, 1]. | | min_volume | 500 | Smaller cavities (ų) are dropped (0-5000). | | max_volume | 5000 | Larger cavities (ų) are dropped; keep it above min_volume (100-20000). | | ph | 7 | pH used to protonate the receptor before docking (0-14). | | batch_size | 2 | Ligands docked per parallel clone (1-500). | | exhaustiveness | 8 | Vina search exhaustiveness per ligand (1-64). | | top_n | 10 | Best-ranked ligands whose poses are written (1-1000). |

References