Cluster Summary

Quality Metrics - Structure

Quality Metrics - Interface

Cluster Summary Table with RMSD QC

Search table:

Cluster Size Distribution

Cluster Stability

HDBSCAN Cluster Persistence Scores

Higher values = more stable/persistent clusters
Bar color intensity = cluster size (log scale)
Based on λ-integral from HDBSCAN's condensed tree

Motif Match Score

Motif Overlap Quality

Shows % of motif residues making contact with DNA/RNA
Higher values = better match to specified motif
Clusters sorted by average match score (best first)
Color: Green (high) to Red (low)

Pose Diversity within Clusters

Intra-Cluster RMSD Distribution

Each point = one pose
X-axis: RMSD from cluster medoid (Å)
Y-axis: Cluster (sorted by size)
Color: By cluster assignment

HDBSCAN Condensed Tree

Cluster Formation & Stability (Right-click image to save)

Vertical: Density (λ) | Horizontal: Cluster Size
Longer bars = more stable clusters
Color-coded by cluster

HDBSCAN Single Linkage Tree

Minimum Spanning Tree (Right-click image to save)

HDBSCAN's hierarchical structure visualization
Scales well to 1000+ poses
Color gradient shows merge distances

Consensus Residues by Cluster

Search Consensus Residues:

All Chains Combined (Color-coded: Red=A, Blue=B)

Per-Chain Hotspot Analysis

Contact Residue Heatmap by Cluster

Intra-cluster Contact Pattern Analysis: Shows which protein residues each structure within a cluster contacts.

Colors represent actual contact distances in Ångströms (red = closer, blue = farther)
Vertical patterns = conserved residues, Diagonal = shifted binding modes
Structures automatically ordered by contact pattern similarity

Select Cluster:

Per-Cluster Hotspot Analysis

Select Cluster:

Hotspot Data

Sequence Alignment Quality Control

Visualize secondary structure and pLDDT confidence for:

Medoid Comparison: Compare secondary structure across cluster medoids
Within Cluster: Examine all structures within a single cluster

Colour Key
pLDDT score: Dark blue (>90), Light blue (70-90), Yellow (50-70), Orange (<50)
Secondary Structure:
α-helix (H, red), 3-10 helix (G, orange), π-helix (I, pink),
β-sheet (E, blue), β-bridge (B, light blue),
Turn (T, green), Bend (S, yellow), Coil/Undefined (-, gray).

Visualization Mode:

Medoid Comparison (across clusters) Within Cluster (all structures)

Select Cluster:

Interface statistics for all structures

Filter by Cluster:

Select a cluster to view only structures in that cluster. Default: Cluster 1

Export PDB Structures

Select Cluster to Export:

📦 Export Cluster PDBsDownloads a ZIP file containing all PDB files for the selected cluster

Interactive 3D Structure Viewer (Molstar)

Filter by Cluster:

Show:

All Structures Medoids Only

Select Structure:

🧬 ClustalDMɑ - AlphaFold2/3 Model Clustering