• Open a new work session and note the confidential ID
• Download the example data (zip file with PDB files)
• Upload data in the "Getting Started: Input data" panel
• Check progression status in the "Job Status" panel

Requirements: Archive (.zip, .tar.gz, .tgz) must contain only structure files (.pdb, .cif, or gzipped versions). One upload per work session.

• Wait for PockDrug processing to complete (status: "PockFlex waiting for parameters")
• Set the number of clusters (recommended value provided based on data after a first job launch)
• Define the Region of Interest (ROI) by listing amino acids (e.g., ILE47, GLY48, GLY49...)
• Adjust the residue display frequency threshold (50%, 75%, or 100%)
• Launch PockFlex clustering analysis

Note: Parameters can be changed and PockFlex re-run within the same work session.

• View druggability repartition histograms (all pockets and detailed levels)
• Explore the global heatmap and clustering dendrogram
• Apply cluster filtering by frequency and druggability thresholds
• Examine individual cluster heatmaps and residue frequency histograms
• Identify persistent vs. transient pockets across the ensemble

Use zoom/rotation controls and filters to focus on specific binding sites.

Pockets Analysis:

• View global PDB statistics (total structures, detected pockets, best/mean druggability scores)
• Examine cluster-level metrics: pocket counts, druggability rates (% druggable pockets ≥ 0.5), intra-cluster distances
• Download CSV table summarising all cluster statistics

Advanced Analysis:

• Identify key residues at different frequency thresholds (25%, 50%, 75%)
• View residue-level appearance counts and druggability distribution across classes
• Distinguish conserved residues (high frequency) from transient ones (low frequency)

Structural Viewer:

• Select a cluster and load its 3D structure to visualise pocket geometry within protein context
• Explore spatial organisation using zoom, rotation, and focus controls
• Toggle display options to show/hide pockets, protein, and switch representation styles

PockDrug Results Download:

• Zip archive containing all estimated pocket PDB files for each conformation
• Includes corresponding conformation PDB files for structural reference
• Use for: structural analysis, molecular docking studies, integration with other computational tools

PockFlex Results Download:

• Zip archive with all clustering visualisations: heatmaps, dendrograms, histograms (.jpg format)
• Includes: global heatmap, cluster-specific heatmaps, residue frequency histograms, druggability distribution plots
• Figures showing pocket similarity, residue composition, and druggability across the ensemble

Understanding the outputs:

• Heatmaps: Black cells = residue presence in pockets; dendrograms = hierarchical clustering based on residue similarity
• Histograms: Residue frequency (x-axis) vs. pocket count (y-axis), colour-coded by druggability levels
• CSV tables: Quantitative data for cluster metrics (pocket counts, druggability rates, distances)
• Druggability scores: 0–1 scale where ≥0.75 = very druggable (red), 0.5–0.75 = quite druggable (pink), 0.25–0.5 = less druggable (light grey), <0.25 = not druggable (grey)