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
3.10.640 MC11110 A0A438AGT4_11110 34-173 5-133 0.81 0.97 0.42 0.52 0.52 0.48 12.3
3.90.1660 MC11101 A0A523AU62_11101 3-92 56-142 0.97 0.38 0.69 0.29 0.29 0.71 34.0
1.10.240 MC11097 A0A1V6EEZ6_11097 4-93 73-178 0.94 0.58 0.4 0.24 0.24 0.53 18.0
4.10.1050 MC10954 A0A177UIB8_10954 9-82 9-79 0.86 0.89 0.25 0.27 0.27 0.5 37.8
3.90.150 MC10922 A0A1J0R4J2_10922 2-202 12-268 0.99 0.78 0.86 0.55 0.55 0.67 18.1
1.10.470 MC10922 A0A1J0RD21_10922 27-158 57-187 0.83 0.5 0.59 0.37 0.37 0.52 20.4
4.10.1200 MC10752 C1E686_10752 2-42 46-85 0.98 0.46 0.34 0.24 0.24 0.63 12.1
1.10.3080 MC10731 A0A1Y1I0T6_10731 2-354 201-556 0.99 0.56 0.98 0.55 0.55 0.91 33.1
1.20.1720 MC10731 A0A1F6L920_10731 2-369 3-398 0.98 0.92 0.63 0.56 0.56 0.43 11.2
1.20.1450 MC10726 A0A800MQN8_10726 10-244 1-235 0.96 1.0 0.95 0.99 0.99 0.96 60.0
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.