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
MC17137 74 217.99 30.52 0.14 83.89 0.3 0.65 0.61 18.17 100.0 PF14219
MC17144 88 175.61 36.49 0.21 84.9 0.2 0.73 0.69 29.52 84.88 CL0039-CL0740-CL0350
MC17145 27 265.22 54.74 0.21 70.98 0.78 0.38 0.67 25.45 86.84 PF19252-PF03343
MC17151 8 60.62 4.64 0.08 94.19 0.27 0.92 0.92 53.36 0.0 UNKNOWN
MC17153 17 420.24 74.64 0.18 83.93 0.19 0.65 0.62 27.88 0.0 UNKNOWN
MC17156 88 112.15 15.86 0.14 90.43 0.21 0.79 0.75 45.3 95.47 PF02772-PF02773-CL0063-CL0145
MC17157 17 102.41 11.7 0.11 83.62 0.21 0.68 0.66 17.08 100.0 PF20391
MC17158 105 210.9 43.33 0.21 90.44 0.19 0.66 0.58 19.71 82.42 PF02965-PF04071-PF02310
MC17159 21 79.71 9.76 0.12 85.7 0.3 0.64 0.84 55.28 100.0 CL0036
MC17160 20 430.15 46.03 0.11 79.23 0.29 0.52 0.55 25.87 91.67 PF12879-CL0474
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.