Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets

- Eight docking programs and sixteen scoring functions were examined.
- Fitted, FlexX and GOLDScore outperformed the other programs here.
- Hydrophilic targets such as factor Xa, Cdk2 kinase and Aurora kinase are amenable to current scoring functions.
- Hydrophobic targets such as COX-2 and Pla2g2a represent challenges to scoring functions.
- No program used was effective for all six protein-ligand data sets sampled in this study.