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
6.20.40 MC8687 L9L6B3_8687 4-47 161-210 0.94 0.22 0.43 0.14 0.14 0.71 12.0
1.20.1270 MC8675 A0A4U5VMQ2_8675 4-79 76-154 0.96 0.11 0.94 0.11 0.11 0.94 70.8
2.60.40 MC8675 A0A182PP65_8675 5-123 211-382 0.96 0.32 0.78 0.2 0.2 0.66 10.9
2.10.250 MC8674 A0A556U1S5_8674 9-145 1-137 0.94 0.75 0.82 0.67 0.67 0.89 63.5
1.10.3430 MC8672 A0A835NII2_8672 29-335 2-308 0.89 0.99 0.89 0.99 0.99 0.94 66.7
3.10.100 MC8664 A0A3L7NFG1_8664 20-122 106-213 0.84 0.5 0.51 0.31 0.31 0.53 16.5
3.90.1580 MC8664 K1Q2E9_8664 1-272 8-293 1.0 0.98 0.98 0.92 0.92 0.95 58.3
2.40.240 MC8663 A0A2D6PV64_8663 6-64 30-86 0.89 0.59 0.61 0.45 0.45 0.61 8.1
2.40.10 MC8663 G2DGP3_8663 3-74 3-81 0.95 0.98 0.8 0.76 0.76 0.75 15.0
2.40.30 MC8663 A0A6M8E2T2_8663 1-63 29-91 0.94 0.69 0.93 0.69 0.69 0.93 57.1
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.