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Ethan Hain edited subsection_Dataset_The_specific_modality__.tex
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Of the 17 targets in the MUV dataset, we identified 10 that had a receptor-ligand structure in the Protein Data Bank (PDB) where the ligand had sub-$\mu$M affinity. The interaction diagrams of these structures are shown in Figure~\ref{targets}. For each of these structures we identified interacting fragments that could potentially serve as anchor fragments. For each target we consider a variety of fragments in order to evaluate the sensitivity of the approach to the choice of fragment. We selected relatively generic functional groups (at most \textbf{X} atoms) that were sufficiently common among both the actives and decoys to yield meaningful results and that were clearly forming interactions with the receptor.
\textbf
\begin{table}
\begin{tabular}{ c c c }
Fragment
SMARTS
Cathg1
c1ccccc1[R]
Cathg2
c1ccccc1[C]
Cathg3
c1ccccc1[!H]
Cathg4
a1aaaaa1[!H]
Cathg5
c1ccccc1[C]
Eralpha_pot1
c1ccccc1O
Eralpha_pot2
c1ccccc1[!H]
Eralpha_pot3
a1aaaaa1[!H]
Eralpha1
c1ccccc1O
Eralpha2
c1ccccc1N
Eralpha3
c1ccccc1[!H]
Eralpha4
a1aaaaa1[!H]
Erbeta1
c1ccccc1O
Erbeta2
c1ccccc1N
Erbeta3
c1ccccc1[!H]
Erbeta4
a1aaaaa1[!H]
Fak1
c1[c,n]cccn1
Fak2
c1cccc([!H])c1
Fak3
a1a([!H])aaaa1
Fak4
n1[c,n][c,n]cc1
Fxia1
a1aaan1
Fxia2
c1[c,n]cc[c,s]1
Fxia3
c1[c,n]cc([!H])[c,s,o]1
Fxia4
a1aaaa1[!H]
Hivrt1
a1aaan1
Hivrt2
c1aacn1
Hivrt3
c1aac([!H])n1
Hivrt4
a1aaaa1[!H]
Hivrt5
c1ccccc1[Cl,O]
Hsp901
c1ccccc1O
Hsp902
c1ccccc1[!H]
Hsp903
a1aaaaa1[!H]
Pka1
c1[c,n]cccn1
Pka2
a1ncccn1
Pka3
a1([!H])ncccn1
Pka4
c1[c,n]c([!H])ccn1
Rho1
c1[c,n]cccn1
Rho2
c1[c,n]c([!H])ccn1 & Fragment & SMARTS & Cathg1 & c1ccccc1[R] & Cathg2 & c1ccccc1[C] & Cathg3 & c1ccccc1[!H] & Cathg4 & a1aaaaa1[!H] & Cathg5 & c1ccccc1[C] & Eralpha_pot1 & c1ccccc1O & Eralpha_pot2 & c1ccccc1[!H] & Eralpha_pot3 & a1aaaaa1[!H] & Eralpha1 & c1ccccc1O & Eralpha2 & c1ccccc1N & Eralpha3 & c1ccccc1[!H] & Eralpha4 & a1aaaaa1[!H] & Erbeta1 & c1ccccc1O & Erbeta2 & c1ccccc1N & Erbeta3 & c1ccccc1[!H] & Erbeta4 & a1aaaaa1[!H] & Fak1 & c1[c,n]cccn1 & Fak2 & c1cccc([!H])c1 & Fak3 & a1a([!H])aaaa1 & Fak4 & n1[c,n][c,n]cc1 & Fxia1 & a1aaan1 & Fxia2 & c1[c,n]cc[c,s]1 & Fxia3 & c1[c,n]cc([!H])[c,s,o]1 & Fxia4 & a1aaaa1[!H] & Hivrt1 & a1aaan1 & Hivrt2 & c1aacn1 & Hivrt3 & c1aac([!H])n1 & Hivrt4 & a1aaaa1[!H] & Hivrt5 & c1ccccc1[Cl,O] & Hsp901 & c1ccccc1O & Hsp902 & c1ccccc1[!H] & Hsp903 & a1aaaaa1[!H] & Pka1 & c1[c,n]cccn1 & Pka2 & a1ncccn1 & Pka3 & a1([!H])ncccn1 & Pka4 & c1[c,n]c([!H])ccn1 & Rho1 & c1[c,n]cccn1 & Rho2 & c1[c,n]c([!H])ccn1 \\
Fragment & SMARTS \\
Cathg1 & c1ccccc1[R] \\
Cathg2 & c1ccccc1[C] \\
Cathg3 & c1ccccc1[!H] \\
Cathg4 & a1aaaaa1[!H] \\
Cathg5 & c1ccccc1[C] \\
Eralpha_pot1 & c1ccccc1O \\
Eralpha_pot2 & c1ccccc1[!H] \\
Eralpha_pot3 & a1aaaaa1[!H] \\
Eralpha1 & c1ccccc1O \\
Eralpha2 & c1ccccc1N \\
Eralpha3 & c1ccccc1[!H] \\
Eralpha4 & a1aaaaa1[!H] \\
Erbeta1 & c1ccccc1O \\
Erbeta2 & c1ccccc1N \\
Erbeta3 & c1ccccc1[!H] \\
Erbeta4 & a1aaaaa1[!H] \\
Fak1 & c1[c,n]cccn1 \\
Fak2 & c1cccc([!H])c1 \\
Fak3 & a1a([!H])aaaa1 \\
Fak4 & n1[c,n][c,n]cc1 \\
Fxia1 & a1aaan1 \\
Fxia2 & c1[c,n]cc[c,s]1 \\
Fxia3 & c1[c,n]cc([!H])[c,s,o]1 \\
Fxia4 & a1aaaa1[!H] \\
Hivrt1 & a1aaan1 \\
Hivrt2 & c1aacn1 \\
Hivrt3 & c1aac([!H])n1 \\
Hivrt4 & a1aaaa1[!H] \\
Hivrt5 & c1ccccc1[Cl,O] \\
Hsp901 & c1ccccc1O \\
Hsp902 & c1ccccc1[!H] \\
Hsp903 & a1aaaaa1[!H] \\
Pka1 & c1[c,n]cccn1 \\
Pka2 & a1ncccn1 \\
Pka3 & a1([!H])ncccn1 \\
Pka4 & c1[c,n]c([!H])ccn1 \\
Rho1 & c1[c,n]cccn1 \\
Rho2 & c1[c,n]c([!H])ccn1 \\
\end{tabular}
\end{table}