# Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening
## 2 Materials and Methods
\begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Target Class** & **DUD–E** & **PDB** & **Protein Name** & **Ligands** & **Decoys** & **Metal** \\  & **Code** & **Code** & **Protein Name** & **Ligands** & **Decoys** & **Metal** \\ \hline cytochrome P450 & **CP2C9** & 1R9O & Cytochrome P450 2C9 & 120 & 7446 & \\  & **CP3A4** & 3 NXU & Cytochrome P450 3A4 & 170 & 11,796 & \\ \hline G protein-coupled receptor & **AA2 AR** & 3 EML & Adenosine A2a receptor & 482 & 31,498 & \\  & **ADRB1** & 2 VT4 & Beta-1 adrenergic receptor & 247 & 15,843 & \\  & **ADRB2** & 3 NY8 & Beta-2 adrenergic receptor & 231 & 14,994 & \\  & **CXCR4** & 3 ODU & C-X-C chemokine receptor type 4 & 40 & 3406 & \\  & **DRD3** & 3 PBL & Dopamine D3 receptor & 480 & 34,022 & \\ \hline Ion channel & **GRIA2** & 3 KGC & glutamate receptor ionotropic AMPA2 & 158 & 11,832 & \\  & **GRIK1** & 1 VSO & glutamate receptor ionotropic kainate 1 & 101 & 6547 & \\ \hline Kinases & **ABL1** & 2 HZI & Tyrosine-protein kinase ABL & 182 & 10,750 & \\  & **AKT1** & 3 CQW & Serine/threonine-protein kinase AKT & 293 & 16,426 & \\  & **AKT2** & 3D0E & Serine/threonine-protein kinase AKT2 & 117 & 6893 & \\  & **BRAF** & 3D4Q & Serine/threonine-protein kinase B-raf & 152 & 9942 & \\  & **CDK2** & 1H00 & Cyclin-dependent kinase 2 & 474 & 27,830 & \\  & **CSF1R** & 3 KRJ & Macrophage colony stimulating factor & 166 & 12,144 & \\  & **EGFR** & 2 RGP & Epidermal growth factor receptor & 545 & 35,020 & \\  & **FAK1** & 3 BZ3 & Focal adhesion kinase 1 & 100 & 5350 & \\  & **IGF1R** & 2 OJ9 & Insulin-like growth factor I receptor & 148 & 9291 & \\  & **JAK2** & 3 LPB & Tyrosine-protein kinase JAK2 & 107 & 6495 & \\  & **KIT** & 3G0E & Stem cell growth factor receptor & 166 & 10,447 & \\  & **KITH** & 2B8T & Thymidine kinase & 57 & 2850 & \\  & **KPCB** & 2 IOE & Protein kinase C beta & 135 & 8692 & \\  & **LCK** & 2 OZ & Tyrosine-protein kinase LCK & 420 & 27,374 & \\  & **MAPK2** & 3M2W & MAP kinase-activated protein kinase 2 & 101 & 6147 & \\  & **MET** & 3 LQ8 & Hepatocyte growth factor receptor & 166 & 11,240 & \\  & **MK01** & 2 OJG & MAP kinase ERK2 & 79 & 4548 & \\  & **MK10** & 2 ZDT & c-Jun N-terminal kinase 3 & 104 & 6599 & \\  & **MK14** & 2 QD9 & MAP kinase p38 alpha & 578 & 35,810 & \\  & **MP2K1** & 3 EQH & Dual specificity mitogen-activated & 121 & 8147 & Mg\({}^{2+}\) \\  & **PLK1** & 2 OWB & Serine/threonine-protein kinase & 107 & 6797 & Zn\({}^{2+}\) \\  & **ROCK1** & 2 ETR & Rho-associated protein kinase 1 & 100 & 6297 & \\  & **SRC** & 3 ELR & tyrosine-protein kinase SRC & 524 & 34,454 & \\  & **TGFR1** & 3 HMM & TGF-beta receptor type I & 133 & 8498 & \\  & **VEGF2** & 2P2I & Vascular endothelial growth factor & 409 & 24,927 & \\  & **WEE1** & 3 BIZ & Serine/threonine-protein kinase & 102 & 6148 & \\ \hline Nuclear receptor & **ANDR** & 2 AM9 & Androgen Receptor & 269 & 14,344 & \\  & **ESR1** & 1 SJ0 & Estrogen receptor alpha & 383 & 20,663 & \\  & **ESR2** & 2 FSZ & Estrogen receptor beta & 367 & 20,182 & \\  & **GCR** & 3 BQD & glucocorticoid receptor & 258 & 14,987 & \\  & **MCR** & 2 AA2 & Mineralocorticoid receptor & 94 & 5146 & \\  & **PPARA** & 2P54 & Peroxisome proliferatorator-activated & & \\  & **PPARD** & 2P54 & Peroxisome proliferatorator-activated & & \\  & **PPARD** & 22 NP & receptor delta & 240 & 12,223 & \\  & **PPARG** & 2 GTK & Peroxisome proliferatorator-activated & & \\  & **PRGR** & 3 KBA & Progesterone receptor & 293 & 15,642 & \\  & **RXRA** & 1 MV9 & retinoid X receptor alpha & 131 & 6935 & \\  & **THB** & 1Q4X & Thyroid hormone receptor beta-I & 103 & 7441 & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Protein targets evaluated in this study as part of DUD–E with indication of the different classes of targets considered.