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
MC34365 13 162.38 18.69 0.12 82.56 0.31 0.63 0.6 19.8 0.0 UNKNOWN
MC34371 10 240.4 22.65 0.09 78.61 0.23 0.56 0.6 28.29 0.0 UNKNOWN
MC34374 6 110.17 8.63 0.08 76.07 0.39 0.72 0.83 51.06 100.0 PF10491
MC34375 10 94.2 10.28 0.11 71.45 0.39 0.59 0.77 29.63 92.86 CL0247-CL0084
MC34376 3 79.0 4.97 0.06 82.22 0.14 0.87 0.82 42.3 100.0 PF21382
MC34379 9 127.56 5.93 0.05 80.15 0.19 0.69 0.78 45.73 0.0 UNKNOWN
MC34383 12 196.83 27.21 0.14 86.91 0.28 0.79 0.77 29.94 0.0 UNKNOWN
MC34390 12 239.58 30.16 0.13 69.38 0.28 0.55 0.71 40.02 100.0 PF05542
MC34391 54 94.76 13.52 0.14 71.35 0.22 0.66 0.76 48.46 97.14 CL0023-CL0137-PF04571
MC34394 22 115.77 16.43 0.14 83.25 0.22 0.83 0.86 38.03 93.81 CL0182-PF03105
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.