deletions | additions       diff --git a/subsection_Dataset_The_specific_modality__.tex b/subsection_Dataset_The_specific_modality__.tex  index 72062e6..63ff01f 100644  --- a/subsection_Dataset_The_specific_modality__.tex  +++ b/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}