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
3.50.40 MC35051 A0A3M1X379_35051 23-193 1-84 0.89 1.0 0.28 0.54 0.54 0.36 11.5
4.10.375 MC34997 A0A7N0VBI8_34997 8-99 1-88 0.92 0.24 0.79 0.22 0.22 0.82 46.7
4.10.372 MC34997 A0A6V7Q3N5_34997 1-89 24-115 1.0 0.22 0.77 0.19 0.19 0.74 44.6
3.90.400 MC34978 A0A4Y8ZR79_34978 1-71 139-209 1.0 0.2 0.99 0.2 0.2 0.99 71.8
2.170.170 MC34902 A0A833NQH4_34902 21-129 1-110 0.84 0.99 0.84 0.97 0.97 0.88 49.0
3.10.40 MC347 A0A1F7USG8_347 9-86 18-125 0.91 0.86 0.52 0.39 0.39 0.48 12.6
3.90.10 MC3467 A0A2V2RIJ1_3467 6-67 72-128 0.91 0.44 0.59 0.34 0.34 0.56 26.1
3.40.580 MC34628 M3LFR6_34628 29-238 2-211 0.8 0.99 0.8 0.98 0.98 0.87 70.0
2.60.450 MC3453 A0A1F3XSN3_3453 28-169 29-191 0.84 0.73 0.28 0.21 0.21 0.57 11.5
6.20.330 MC3443 A0A2V0NRU5_3443 2-67 445-510 0.98 0.1 0.9 0.1 0.1 0.91 40.9
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.