DockQ
TrustBSolid metric for comparing PPI prediction methods head to head. The continuous scale is more informative than CAPRI's categorical ratings. But like all docking metrics, it rewards geometric accuracy without asking whether the predicted complex is biologically meaningful.
What It Measures
Quality of protein-protein docking predictions. Combines interface RMSD, ligand RMSD, and fraction of native contacts into a single continuous score from 0 to 1.
What It Doesn't Measure
Protein-ligand docking, conformational flexibility, or the biological relevance of the predicted interface.
Maintainer
Wallner Lab (Linköping University)
https://github.com/bjornwallner/DockQ →Known Limitations
Single-score aggregation can mask important failure modes. A medium DockQ score might mean the interface is partially right or completely wrong in a different way. Doesn't handle multi-body docking well.