DPCstruct Metaclusters

⬡ Domain Classification in Structural Space
Properties CATH SCOP

The DPCstruct pipeline applied the Density Peak Clustering (DPC) algorithm to roughly 15 million representative AlphaFold2- predicted structures from the Foldseek Cluster database (a representative set of the AlphaFold Database, AlphaFoldDB v4.0), producing 28,246 structural metaclusters without any manual annotation. Because protein structure is more conserved than sequence over evolutionary time, DPCstruct recovers remote homologs, including proteins sharing a common fold at less than 30% sequence identity, that purely sequence-based methods typically miss.

Use the toggle buttons to switch between the Properties view (intrinsic structural metrics and Pfam annotations), the CATH fold annotations, or the SCOP fold annotations. Click any MCID to open its detail page, where you can explore the sequences and launch the integrated PDBe-Mol* 3D viewer.

MCID Size Avg. Len. Len. Std Len. Ratio pLDDT Disorder TM-Score lDDT pIdent Pfam Score Pfam Labels
MC28881 34 136.94 24.34 0.18 80.17 0.35 0.62 0.75 28.81 100.0 PF05591
MC28885 11 212.91 22.26 0.1 77.06 0.25 0.6 0.65 24.52 0.0 UNKNOWN
MC28890 31 151.77 21.05 0.14 82.52 0.2 0.67 0.61 19.78 100.0 PF16117
MC28895 11 115.91 9.1 0.08 91.47 0.24 0.77 0.7 26.12 0.0 UNKNOWN
MC28898 22 77.45 8.95 0.12 90.03 0.39 0.81 0.77 31.96 100.0 CL0187
MC28902 538 150.19 25.8 0.17 86.36 0.22 0.6 0.53 16.95 95.89 CL0441-PF17057-PF03691
MC28903 19 182.37 24.23 0.13 74.88 0.25 0.64 0.72 30.7 0.0 UNKNOWN
MC28905 10 199.0 24.13 0.12 71.0 0.19 0.45 0.6 24.54 0.0 UNKNOWN
MC28906 3 78.33 4.99 0.06 80.57 0.31 0.83 0.81 41.45 0.0 UNKNOWN
MC28907 11 108.36 17.23 0.16 83.68 0.17 0.79 0.75 40.94 0.0 UNKNOWN
Legend
  • A. Metacluster Structural Properties :
  • MCID: Unique identifier per metacluster.
  • Size: Number of structural domain members.
  • Avg. Len.: Mean domain length of all members (amino acids).
  • Len. Std: Standard deviation of domain lengths.
  • Len. Ratio: Ratio of standard deviation to average domain length.
  • pLDDT: Mean AlphaFold2 confidence score (predicted Local Distance Difference Test) across all members.
  • Disorder: Mean fraction of residues predicted as intrinsically disordered.
  • TM-Score: Mean intra-cluster pairwise alignment Template Modeling score, averaged over all pairs, using the maximum between TM-score normalized by query or target to account for size differences.
  • lDDT: Mean intra-cluster local Distance Difference Test score (local structural similarity).
  • pIdent: Mean intra-cluster sequence similarity (%).
  • B. Pfam Annotations:
  • Pfam Score: Global Pfam Score quantifying the agreement between the metacluster and Pfam domains.
  • Pfam Labels: Assigned Pfam labels (clans or families). Displayed as UNKNOWN (representing 'dark matter') if no Pfam domains are assigned to the metacluster.