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
3.30.2160 MC9905 A0A7H4MW51_9905 3-73 12-76 0.91 0.47 0.26 0.17 0.17 0.51 9.5
1.20.1580 MC9630 C2NRS3_9630 1-132 78-209 0.95 0.63 0.93 0.62 0.62 0.87 50.0
1.10.3990 MC957 A0A521GNK4_957 7-95 2-84 0.82 0.98 0.56 0.69 0.69 0.55 24.4
3.90.1740 MC9528 A0A7S0DPV3_9528 6-201 10-135 0.95 0.52 0.5 0.43 0.43 0.51 11.2
3.90.1140 MC9528 A0A816R5E1_9528 1-180 13-193 0.99 0.94 0.97 0.91 0.91 0.95 87.2
2.20.80 MC95 A0A7R9DN90_95 2-208 400-600 0.82 0.33 0.58 0.26 0.26 0.65 13.1
2.30.230 MC95 A0A3B4CDQ0_95 7-262 2-244 0.97 0.38 0.86 0.36 0.36 0.78 33.2
1.20.1520 MC9337 A0A402F1A5_9337 1-120 1-120 0.96 0.99 0.95 0.98 0.98 0.98 86.6
1.10.555 MC931 A0A1V9Z9Y6_931 5-199 79-302 0.93 0.74 0.61 0.44 0.44 0.52 13.5
3.30.1560 MC93 A0A7Y5MQG8_93 1-128 1-114 0.9 0.56 0.6 0.45 0.45 0.61 11.6
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.