Cavity Analysis across a Conformational Ensemble

Detect and filter cavities with fpocket on every structure of a conformational ensemble in parallel, then rank the models by their best cavity's volume, druggability and score.

by Temple Compute

Run Cavity Analysis across a Conformational Ensemble on Horus

W-31 · Cavity Analysis

Detect and filter cavities with fpocket on every structure of a conformational ensemble in parallel, then rank the models by their best cavity's volume, druggability and score.

Domain: BioExcel Building Blocks

Overview

Detects and ranks druggable cavities across a conformational ensemble (MD cluster representatives, NMR models or any set of related structures). fpocket runs on each model, cavities are filtered by score, druggability and volume, and models are ranked by their best cavity. The result indicates which conformation to dock into with W-30. The workflow has 3 tasks.

Pipeline

prepare_models                                  Wrap each structure in its own model folder
analyze[00..NN]                                 One clone per model: extract_molecule, fpocket_run, fpocket_filter, optional residue-distance filter
summarize                                       Rank models by volume, druggability and score

Inputs / Outputs

Outputs (results/):

A model with no cavity inside the filter windows is absent from the summaries and counted in cavity_report.json. A failing model is recorded in status.json and does not fail the run.

Parameters

| id | Default | Meaning | |---|---|---| | structures | examples/structures/ | Folder of PDB models (a single .pdb also works). | | min_druggability | 0.2 | Cavities below this fpocket druggability score are dropped (0-1). | | min_volume | 100 | Cavities smaller than this are dropped (0-5000). | | max_volume | 5000 | Cavities larger than this are dropped (100-20000); keep above min_volume. | | residue_selection | empty | MDAnalysis selection of a site of interest (e.g. resid 31 or resid 21); only cavities within 10 Å of its centre of mass are kept. Empty keeps every cavity. |

References