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
3.90.520 MC5640 U6HAS1_5640 1-125 17-145 0.97 0.87 0.55 0.49 0.49 0.46 10.0
3.10.670 MC56383 A0A4Q6EZ94_56383 3-142 31-175 0.88 0.69 0.5 0.4 0.4 0.45 15.1
3.90.1200 MC56050 A0A485CQ32_56050 7-211 6-281 0.97 0.88 0.56 0.4 0.4 0.47 15.3
2.60.520 MC55775 A0A2K3JD92_55775 17-120 5-101 0.86 0.28 0.53 0.22 0.22 0.52 13.5
3.40.210 MC5570 A0A160T5I5_5570 1-100 3-229 0.93 0.84 0.73 0.3 0.3 0.67 10.9
6.20.80 MC5565 A0A813GGJ4_5565 5-61 51-123 0.9 0.46 0.42 0.21 0.21 0.59 14.6
3.30.2060 MC5565 A0A6D0EXZ4_5565 1-90 10-99 1.0 0.76 1.0 0.75 0.75 0.99 100.0
1.10.3710 MC5560 A0A7W1MMU7_5560 2-74 103-191 0.97 0.46 0.89 0.36 0.36 0.84 31.1
3.90.1850 MC55173 A0A812GJF2_55173 40-466 1-386 0.84 0.99 0.49 0.61 0.61 0.42 12.0
3.20.80 MC55173 A0A833X6G8_55173 4-125 148-259 0.88 0.43 0.51 0.3 0.3 0.54 17.4
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.