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
MC23531 12 203.67 17.6 0.09 68.01 0.23 0.5 0.77 32.73 100.0 CL0229
MC23532 26 91.46 20.19 0.22 90.3 0.18 0.83 0.77 41.9 100.0 CL0177
MC23536 65 141.25 25.71 0.18 68.54 0.43 0.4 0.77 30.4 77.72 CL0229-PF01754
MC23537 11 226.18 25.82 0.11 76.33 0.29 0.64 0.82 33.75 100.0 PF14775
MC23538 27 153.89 26.05 0.17 78.66 0.63 0.35 0.77 29.93 0.0 UNKNOWN
MC23542 34 161.29 15.69 0.1 88.17 0.28 0.72 0.72 25.0 100.0 CL0131
MC23546 28 122.18 19.84 0.16 87.17 0.21 0.74 0.67 21.89 0.0 UNKNOWN
MC23549 9 115.78 8.64 0.07 71.52 0.51 0.42 0.74 45.91 0.0 UNKNOWN
MC23550 94 243.22 39.11 0.16 89.5 0.22 0.75 0.66 23.71 100.0 PF01259
MC23551 21 152.24 10.75 0.07 73.3 0.22 0.46 0.74 34.37 90.07 CL0614-CL0466
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.