Table 1.
Structure-based docking metrics
| Metric name | Short description |
|---|---|
| PlantsFull | PLANTS score (with anchor weight) (Korb et al., 2006) |
| Plants | PLANTS ChemPLP score (without weight) |
| PlantsLR | PLANTS pKa (calculated by linear regression on PDBbind) |
| MedusaScore | Medusa original score (Yin et al., 2008) |
| MedusaLR | MedusaScore pKa (calculated by linear regression on PDBbind) |
| XScore | XScore affinity score (pKa) (Wang et al., 2002) |
| DSX | DSX original score (Neudert and Klebe, 2011) |
| DSXLR | DSX pKa (calculated by linear regression on PDBbind) |
| AtomeScore | @TOME pKa = mean(PLANTS, XScore, MedusaScore, DSX) |
| Tanimoto | Similarity between candidate ligand and anchor ligand |
| AtomSA | S.A. @TOME score |
| QMean | QMean score of receptor model |
| AnchKd | Affinity calculated between receptor/anchor (pKa) |
| AnchorFit | Candidate/ligand superimposition score (PLANTS software) |
| LigandEnergy | Internal energy of ligand (AMMP force field) |
| LPC | LPC software score (receptor/ligand complementarity function) |
| PSim | Similarity to receptor/ligand interaction profile in PDB template |
| CpxQuality | Complex quality consensus score |
| LPE | Ligand Position Error (SVM multi-variable linear regression) |