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.

CATH Fold MCID DPC Target Q.Range T.Range Q.Cov T.Cov Q.TM-Score T.TM-Score A.TM-Score lDDT pIdent
1.10.1320 MC13739 A0A3N5WCG0_13739 28-311 6-283 0.89 0.98 0.74 0.82 0.82 0.69 23.4
1.10.3120 MC1363 A0A117ME61_1363 13-93 3-99 0.87 0.84 0.55 0.46 0.46 0.51 7.3
1.10.489 MC13622 A0A409VHX2_13622 14-273 1-260 0.8 1.0 0.8 1.0 1.0 0.9 70.7
1.10.3460 MC13415 A0A2G3A7J8_13415 1-203 31-233 1.0 0.87 1.0 0.87 0.87 1.0 98.5
1.10.599 MC13311 A0A7V2X9N0_13311 30-201 9-186 0.83 0.95 0.77 0.85 0.85 0.79 41.1
3.90.280 MC1323 A0A6I8UQ17_1323 1-185 230-413 1.0 0.44 0.98 0.44 0.44 0.93 57.2
2.60.250 MC13059 A0A017T269_13059 9-295 1-249 0.96 0.99 0.45 0.52 0.52 0.43 11.4
2.40.310 MC12974 C4XMM5_12974 11-109 21-118 0.91 0.83 0.55 0.52 0.52 0.5 15.4
1.10.1790 MC1294 B0NY60_1294 2-98 35-133 0.98 0.45 0.89 0.42 0.42 0.79 25.2
4.10.490 MC12747 P00266_12747 1-62 1-63 1.0 1.0 0.97 0.95 0.95 0.95 71.4
Legend
  • Agreement between CATH Folds and DPCstruct Metacluster Domains:
  • CATH Fold: CATH fold identifier.
  • MCID: DPCstruct metacluster identifier.
  • DPC Target: Target DPCstruct protein domain.
  • Q./T.Range: Amino acid coordinate ranges for query and target.
  • Q./T.Cov: Coverage metrics indicating how much of each domain was covered in the alignment.
  • A.TM-Score: Template Modeling score of the structural alignment (0-1).
  • lDDT: Local Distance Difference Test score.
  • pIdent: Percent sequence identity between query and target.