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
3.30.930 MC7935 A0A2U1UYA1_7935 4-176 2-165 0.86 0.99 0.47 0.54 0.54 0.39 14.4
3.30.540 MC7935 A0A219AND3_7935 9-120 2-84 0.84 0.38 0.43 0.28 0.28 0.0 9.2
3.30.1460 MC7935 A0A520DJJ2_7935 8-123 49-201 0.9 0.76 0.49 0.34 0.34 0.53 11.1
3.30.920 MC7935 A0A829LIP8_7935 1-148 4-151 1.0 0.89 1.0 0.88 0.88 0.99 100.0
1.10.275 MC7929 K9GH78_7929 1-104 5-94 0.8 0.95 0.52 0.69 0.69 0.5 28.0
2.20.70 MC7925 A0A7I2YQL2_7925 2-58 49-105 0.98 0.45 0.97 0.45 0.45 0.98 100.0
3.30.160 MC7921 A0A423TFS2_7921 3-99 1-97 0.95 0.99 0.85 0.88 0.88 0.79 31.9
3.30.1420 MC7919 A0A7Y0H1M7_7919 3-41 22-61 0.95 0.24 0.37 0.12 0.12 0.56 25.0
3.90.1440 MC7919 A0A7C4YTL1_7919 1-122 3-139 1.0 0.57 0.91 0.48 0.48 0.84 35.0
3.30.280 MC79 A0A430FLE9_79 1-100 1-100 1.0 0.96 0.99 0.95 0.95 0.96 56.0
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.