# 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** & \begin{tabular}{c} **DUD–E** \\ **Code** \\ \end{tabular} & \
\begin{tabular}{c} **PDB** \\ **Code** \\ \end{tabular} &
\begin{tabular}{c} **Protein Name** \\ \end{tabular} & **Ligands** & **Decoys** & **Metal** \\ \hline Proteases & **ACE** & 3 BKL & Angiotensin-converting enzyme & 282 & 16,864 & Zn\({}^{2+}\) \\
**ADA17** & 2O10 & protease & 532 & 35,809 & Zn\({}^{2+}\) \\
**BACE1** & 3L5D & Beta-secretase 1 & 283 & 18,082 & \\
**CASP3** & 2 CNK & Caspase-3 & 199 & 10,692 & \\
**DPP4** & 2I78 & Dippeptidyl peptidase IV & 533 & 40,916 & \\
**FA10** & 3K16 & Coagulation factor X & 537 & 20,023 & \\
**FA7** & 1W7X & Coagulation factor VII & 114 & 6245 & \\
**HIVPR** & 1 XL2 & human immunodeficiency virus type 1 & 536 & 35,688 & \\
**LKHA4** & 3 CHP & Leukotriene A4 hydrolase & 171 & 9448 & Zn\({}^{2+}\) \\
**MMP13** & 830C & Matrix metalloproteinase 13 & 572 & 37,126 & Zn\({}^{2+}\) \\
**RENT** & 3G62 & Renin & 104 & 6956 & \\
**THRB** & 1 YPE & Thrombin & 461 & 26,948 & \\
**TRY1** & 2 AYW & Trypin I & 449 & 25,914 & \\
**TRYB1** & 2 ZEC & Typratase beta-I & 148 & 7643 & \\
**UROK** & 1 SQT & Urokinase-type plasminogen activator & 162 & 9841 & \\ \hline Miscellaneous & **AMPC** & 1L2S & Beta-lactamase & 48 & 2832 & \\
**HIVRT** & 3 NF7 & human immunodeficiency virus type 1 & 100 & 6644 & \\
**KIF11** & 3 CJO & Kinesin-like protein 1 & 116 & 6848 & Mg\({}^{2+}\) \\ \hline Other & **ACES** & 1\_e66 & Acetylcholinesteraseterase & 453 & 26,234 & \\
**ADA** & 2E1W & Adenosine deaminase & 93 & 5449 & Zn\({}^{2+}\) \\
**ALDR** & 2 HV5 & Aldose reductase & 159 & 8995 & \\
**AOFB** & 1S3B & Monoamine oxidase B & 122 & 6900 & \\
**CAH2** & 1 BCD & Carbonic anhydrase II & 492 & 31,132 & Zn\({}^{2+}\) \\
**COMT** & 3 BWM & Catechol O-methyltransferase transferase & 41 & 3848 & Mg\({}^{2+}\) \\
**DEF** & 1 LRU & Peptide deformylase & 102 & 5696 & Zn\({}^{2+}\) \\
**DHII** & 3 FRJ & 11-beta-hydroxysteroid & 330 & 19,340 & \\
**FGFR1** & 3C4F & Fibroblast growth factor receptor 1 & 139 & 4206 & \\
**DYR** & 3 NXO & Dihydrofolate reductase & 231 & 17,170 & \\
**FABP4** & 2 NNQ & Fatty acid binding protein adipocyte & 47 & 2749 & \\
**FKB1A** & 1J4H & FK506-binding protein 1A & 111 & 5800 & \\
**FNTA** & 3E37 & protein farnesyltransferasease/gervnyl & 592 & 51,430 & Zn\({}^{2+}\) \\
**FPPS** & 1 ZW5 & Farnesyl diphosphate synthase & 85 & 8822 & Mg\({}^{2+}\) \\
**GLCM** & 2 VF3 & beta glucocereboside & 54 & 3799 & \\
**HDAC2** & 3 MAX & histone deacetylase 2 & 185 & 10,300 & Zn\({}^{2+}\) \\
**HDAC8** & 3F07 & histone deacetylase 8 & 170 & 10,448 & Zn\({}^{2+}\) \\
**HIVNT** & 3 NF7 & human immunodeficiency virus type 1 & 100 & 6644 & \\
**HMDH** & 3 CCW & HMG-CoA reductase & 170 & 8743 & \\
**HS90A** & 1 UYG & heat shock protein HSP 90-alpha & 88 & 4848 & \\
**HXX4** & 3F0M & hexokinase type IV & 92 & 4696 & \\
**INHA** & 2H7L & Enoyl-[-]carrier-protein] reductase & 44 & 2300 & \\
**ITAL** & 2 ICA & Leukocyte adhesion glycoprotein & 138 & 8487 & \\
**NOS1** & 1 QW6 & Nitric-oxide synthase, brain & 100 & 8050 & Zn\({}^{2+}\) \\
**NRAM** & 1B9V & Neutralinase & 98 & 6199 & \\
**PA2 GA** & 1 KVO & Phospholipases A2 group IIA & 99 & 5146 & \\
**PARP1** & 3L3M & Poly [ADP-ribose] polymerase-1 & 508 & 30,035 & \\
**PDESA** & 1 UDT & Phosphodiesterase 5A & 398 & 27,521 & \\
**PGH1** & 2 OYU & Cyclooxygenase-1 & 195 & 10,797 & \\
**PGH2** & 3 LNN & Cyclooxygenase-2 & 435 & 23,135 & \\
**PNPH** & 3 BGS & Purine nucleoside phosphorylase & 103 & 6950 & \\
**PTN1** & 2 AZR & Protein-tyrosine phosphatase 1B & 130 & 7243 & \\
**PUR2** & 1 NJS & GAR transformylase & 50 & 2694 & \\
**PYGM** & 1C8K & Muscle glycogen phosphorylase & 77 & 3940 & \\
**PYRD** & 1D3G & Dihydroororate dehydrogenase & 111 & 6446 & \\
**SAHH** & 1L1A & adenosylhomocysteine & 63 & 3450 & \\
**TYSY** & 1 SYN & Thymidylate synthase & 109 & 6738 & \\
**XIAP** & 3 HL5 & Inhibitor of apoptosis protein 3 & 100 & 5145 & Zn\({}^{2+}\) \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Cont.