## 4 Examples of Commercial Targeted Libraries
### Protease-Inhibitor-Focused Libraries
The remaining compounds were selected by using molecular docking into different protease targets and confirming the results by molecular dynamics simulations. PAINS, toxic and reactive compounds were excluded from the library. For each library described, we performed an analysis of the most common molecular descriptors: Molecular Weight (MW), Total Polar Surface Area (TPSA), SlogP, number of hydrogen bond acceptors (HBA), number of hydrogen bond donors (HBD), number of rings present and the number of rotatable bonds (Table 4). Compound retention when passing through each individual filter was assessed, as well (Table 5), with the results for joined filter provided in Figure 9. \begin{table}
\begin{tabular}{c c c c c c c c c} \hline \hline
**Database** & **No. of** & & & & & & & **No. of** \\
**Name** & **Compounds** & & & & & & & & **Rings** & **Rotatable** \\  & & & & & & & & & **Bonds** \\ \hline ApexBio & 824 & 348 \(\pm\) 181 & 96 \(\pm\) 59 & 1.9 \(\pm\) 2.8 & 5.0 \(\pm\) 3.2 & 2.5 \(\pm\) 2.0 & 2.5 \(\pm\) 1.7 & 5.2 \(\pm\) 4.5 \\ Asinex & 6640 & 383 \(\pm\) 34 & 79 \(\pm\) 18 & 2.9 \(\pm\) 1.0 & 5.3 \(\pm\) 1.3 & 0.9 \(\pm\) 0.7 & 3.7 \(\pm\) 0.6 & 4.7 \(\pm\) 1.5 \\ Chemdiv & 41,801 & 406 \(\pm\) 63 & 74 \(\pm\) 20 & 3.6 \(\pm\) 1.2 & 5.0 \(\pm\) 1.6 & 1.1 \(\pm\) 0.7 & 3.7 \(\pm\) 0.8 & 5.4 \(\pm\) 1.8 \\ Enamine & 117 & 336 \(\pm\) 167 & 90 \(\pm\) 58 & 2.2 \(\pm\) 2 & 4.4 \(\pm\) 2.6 & 2.0 \(\pm\) 1.8 & 2.5 \(\pm\) 1.5 & 4.5 \(\pm\) 4.4 \\ LifeChemicals & 25,535 & 390 \(\pm\) 70 & 81 \(\pm\) 22 & 3.0 \(\pm\) 1.4 & 5.3 \(\pm\) 1.7 & 1.0 \(\pm\) 0.7 & 3.3 \(\pm\) 0.9 & 4.9 \(\pm\) 1.9 \\ Ottawa & 8034 & 352 \(\pm\) 71 & 79 \(\pm\) 23 & 3.0 \(\pm\) 1.2 & 4.6 \(\pm\) 1.6 & 1.4 \(\pm\) 0.9 & 3.2 \(\pm\) 1.1 & 4.5 \(\pm\) 1.8 \\ SelleckChem & 227 & 409 \(\pm\) 168 & 106 \(\pm\) 52 & 2.4 \(\pm\) 2 & 5.45 \(\pm\) 2.6 & 2.4 \(\pm\) 1.7 & 2.9 \(\pm\) 1.7 & 6.2 \(\pm\) 4.4 \\ TargetMol & 295 & 410 \(\pm\) 183 & 107 \(\pm\) 60 & 2.4 \(\pm\) 2.2 & 5.6 \(\pm\) 3.1 & 2.5 \(\pm\) 2.0 & 3.0 \(\pm\) 1.8 & 5.9 \(\pm\) 4.5 \\ Joined Protease & & & & & & & & \\ Inhibitor & 83,473 & 394 \(\pm\) 70 & 77 \(\pm\) 23 & 3.3 \(\pm\) 1.3 & 5.0 \(\pm\) 1.7 & 1.1 \(\pm\) 0.8 & 3.5 \(\pm\) 0.9 & 5.1 \(\pm\) 1.9 \\ Databases & & & & & & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 4: Analysis of the most important descriptors for the protease-inhibitor-targeted library. \begin{table}
\begin{tabular}{c c c c c c c c} \hline \hline  & **ApexBio** & **Asinex** & **Chemdiv** & **Enamine** & **LifeChemicals** & **Otava** & **SelleckChem** & **TargetMol** \\ \hline Unfiltered & 824 & 6640 & 41,801 & 117 & 25,535 & 8034 & 227 & 295 \\ \hline Isolated & & & & & & & \\ filter: & & & & & & & \\ \hline REOS & 397(48\%) & 273(4\%) & 2151(5\%) & 54(46\%) & 3583(14\%) & 1025(13\%) & 110(48\%) & 146(49\%) \\ PAINS & 58(7\%) & 129(2\%) & 1060(3\%) & 7(6\%) & 430(2\%) & 307(4\%) & 7(3\%) & 16(5\%) \\ Aggregators & 294(36\%) & 3254(49\%) & 29,313(70\%) & 36(31\%) & 14,059(55\%) & 4216(52\%) & 88(39\%) & 118(40\%) \\ Lipinski & 113(14\%) & 0(0\%) & 1045(2\%) & 11(9\%) & 409(2\%) & 2(\(\sim\)0\%) & 37(16\%) & 55(19\%) \\ Ro5 & & & & & & & & \\ All filters & 743(90\%) & 5019(76\%) & 37,137(89\%) & 106(91\%) & 23,215(91\%) & 6987(87\%) & 208(92\%) & 272(92\%) \\ \hline \hline \end{tabular}
\end{table} 
Table 5: Analysis of the attrition rate of various filters for the protease-inhibitor-targeted library.