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
MC399 9 185.89 21.26 0.11 75.85 0.78 0.55 0.76 33.17 0.0 UNKNOWN
MC400 29 104.66 10.66 0.1 70.88 0.37 0.8 0.78 37.26 100.0 CL0706
MC401 24 177.75 16.42 0.09 69.35 0.4 0.49 0.69 23.73 0.0 UNKNOWN
MC402 6 65.17 8.03 0.12 88.46 0.19 0.57 0.86 45.53 0.0 UNKNOWN
MC403 20 163.4 23.59 0.14 89.3 0.18 0.75 0.7 32.97 0.0 UNKNOWN
MC404 23 178.74 16.97 0.09 75.09 0.29 0.7 0.72 28.53 0.0 UNKNOWN
MC405 10 177.5 14.42 0.08 83.69 0.21 0.72 0.7 23.19 0.0 UNKNOWN
MC406 53 143.28 27.49 0.19 78.77 0.3 0.7 0.71 32.32 98.68 PF02441-PF11913
MC407 16 173.5 12.84 0.07 79.66 0.24 0.83 0.78 42.1 0.0 UNKNOWN
MC408 30 159.4 21.82 0.14 86.78 0.23 0.67 0.61 23.69 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.