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
4.10.320 MC4357 A0A819VZS2_4357 1-38 315-357 0.86 0.12 0.66 0.1 0.1 0.66 23.2
3.90.1800 MC4357 A0A2G2VNH0_4357 2-85 123-252 0.82 0.39 0.42 0.13 0.13 0.6 10.6
3.90.980 MC4352 D6RI55_4352 1-155 13-175 1.0 0.87 0.99 0.82 0.82 0.98 93.8
1.20.1600 MC4342 A0A1S3W6R2_4342 80-429 95-374 0.82 0.72 0.16 0.17 0.17 0.0 12.8
2.40.37 MC43361 A0A814LU06_43361 18-138 1-121 0.82 0.99 0.8 0.97 0.97 0.85 38.8
3.90.650 MC43203 A0A0N0Z2L8_43203 1-174 26-199 0.99 0.83 0.99 0.83 0.83 0.98 91.9
1.10.645 MC43084 A0A383W916_43084 1-377 8-391 1.0 0.96 0.97 0.92 0.92 0.85 42.9
3.10.680 MC42976 A0A452YKQ3_42976 2-147 18-163 0.84 0.89 0.84 0.89 0.89 0.85 69.1
1.10.3290 MC4287 A0A6L8LPT1_4287 47-301 2-245 0.84 1.0 0.76 0.93 0.93 0.84 54.5
2.90.20 MC42832 A0A1D3TGD0_42832 10-154 2-146 0.94 0.84 0.85 0.76 0.76 0.83 39.3
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.