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
3.30.9 MC57403 A0A540MCC7_57403 19-130 1-96 0.86 1.0 0.4 0.52 0.52 0.47 9.3
3.90.1340 MC57400 A0A1M6GBQ8_57400 5-56 16-85 0.93 0.69 0.84 0.48 0.48 0.81 15.7
3.30.430 MC5740 A0A178BBT5_5740 1-105 27-141 1.0 0.8 0.9 0.67 0.67 0.79 30.7
3.30.2240 MC5739 A0A645AWR4_5739 2-61 16-72 0.8 0.78 0.29 0.3 0.3 0.5 11.6
4.10.87 MC57359 G0QN32_57359 1-46 3-47 0.85 0.34 0.55 0.28 0.28 0.68 23.9
6.10.340 MC57356 A0A7X2ZDE3_57356 4-100 9-105 0.95 0.29 0.81 0.27 0.27 0.87 18.5
1.20.1230 MC57356 A0A090PB48_57356 15-233 88-301 0.93 0.55 0.53 0.35 0.35 0.58 17.4
1.10.880 MC5710 A0A1C9KCY3_5710 1-41 58-100 1.0 0.27 0.87 0.25 0.25 0.83 58.1
3.10.105 MC56990 A0A3R9T492_56990 10-144 244-386 0.86 0.26 0.45 0.14 0.14 0.52 25.8
3.30.1770 MC5695 A0A077ZQ14_5695 3-97 92-210 0.97 0.31 0.85 0.23 0.23 0.75 25.2
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.