Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
Fig 3
Target prediction accuracy comparison of network-based and ligand-based approaches.
(A) Comparison of the overall target prediction accuracy based on the top hit, top five hits and top ten hits analyzed by CSNAP or the SEA approach using 206 benchmark compounds comprised of six major drug classes (ACE, CDK2, HIVRT, HMGA, HSP90 and PARP). The result shows that CSNAP provides a substantial improvement in target prediction accuracy over the traditional ligand-based approach by pair-wise chemical similarity comparison. (B and C) Detailed target prediction accuracy comparison breakdown of each of the six drug classes predicted by (B) CSNAP and (C) SEA approach respectively. The comparison showed that CSNAP provided a greater success rate at identifying the major targets of promiscuous ligands such as CDK2 and ACE inhibitors, which resulted in low prediction accuracies by the traditional ligand-based method.