diff --git "a/notebooks/best_fingerprint_search.ipynb" "b/notebooks/best_fingerprint_search.ipynb"
--- "a/notebooks/best_fingerprint_search.ipynb"
+++ "b/notebooks/best_fingerprint_search.ipynb"
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
@@ -45,7 +45,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 18,
"metadata": {},
"outputs": [
{
@@ -54,7 +54,7 @@
"771"
]
},
- "execution_count": 13,
+ "execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
@@ -73,6 +73,7 @@
" test_df = active_df.sample(frac=test_split, random_state=42)\n",
" return test_df.index\n",
"\n",
+ "protac_df['pDC50'] = -np.log10(protac_df['DC50 (nM)'] * 1e-9)\n",
"active_df = protac_df[protac_df[active_col].notna()].copy()\n",
"test_split = 0.1\n",
"test_indices = get_random_split_indices(active_df, test_split)\n",
@@ -80,6 +81,2080 @@
"len(train_val_df)"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "6.935675466781487"
+ ]
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# Get the mean of pDC50 for the active PROTACs\n",
+ "mean_pDC50 = active_df['pDC50'].mean()\n",
+ "mean_pDC50"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "Index(['Compound ID', 'Uniprot', 'Smiles', 'E3 Ligase', 'InChI', 'InChI Key',\n",
+ " 'Molecular Weight', 'Heavy Atom Count', 'Ring Count',\n",
+ " 'Rotatable Bond Count', 'Topological Polar Surface Area',\n",
+ " 'Hydrogen Bond Acceptor Count', 'Hydrogen Bond Donor Count',\n",
+ " 'Cell Type', 'Treatment Time (h)', 'DC50 (nM)', 'Dmax (%)', 'Active',\n",
+ " 'Article DOI', 'Comments', 'Database', 'Molecular Formula', 'cLogP',\n",
+ " 'Target', 'PDB', 'Name', 'Assay (DC50/Dmax)', 'Exact Mass', 'XLogP3',\n",
+ " 'Target (Parsed)', 'POI Sequence', 'E3 Ligase Uniprot',\n",
+ " 'E3 Ligase Sequence', 'Cell Line Identifier', 'Active - OR',\n",
+ " 'Active (Dmax 0.6, pDC50 6.0)', 'pDC50'],\n",
+ " dtype='object')"
+ ]
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "train_val_df.columns"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "
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+ "\n",
+ "
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+ " \n",
+ " \n",
+ " | \n",
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+ " Active (Dmax 0.6, pDC50 6.0) | \n",
+ " DC50 (nM) | \n",
+ " Dmax (%) | \n",
+ " Uniprot | \n",
+ " E3 Ligase | \n",
+ " Assay (DC50/Dmax) | \n",
+ " Article DOI | \n",
+ "
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+ " \n",
+ " \n",
+ " \n",
+ " 69 | \n",
+ " C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CC... | \n",
+ " H1975/WR | \n",
+ " True | \n",
+ " 5.9 | \n",
+ " 100.0 | \n",
+ " P00533 | \n",
+ " VHL | \n",
+ " NaN | \n",
+ " 10.1016/j.ejmech.2020.112199 | \n",
+ "
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+ " \n",
+ " 1229 | \n",
+ " C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CC... | \n",
+ " A431 siYAP | \n",
+ " False | \n",
+ " 2000.0 | \n",
+ " NaN | \n",
+ " P00533 | \n",
+ " VHL | \n",
+ " Degradation of EGFR in A431 cells after 16 h t... | \n",
+ " 10.1016/j.ejmech.2020.112199 | \n",
+ "
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+ " \n",
+ "
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+ "
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+ ],
+ "text/plain": [
+ " Smiles Cell Line Identifier \\\n",
+ "69 C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CC... H1975/WR \n",
+ "1229 C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CC... A431 siYAP \n",
+ "\n",
+ " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n",
+ "69 True 5.9 100.0 P00533 VHL \n",
+ "1229 False 2000.0 NaN P00533 VHL \n",
+ "\n",
+ " Assay (DC50/Dmax) \\\n",
+ "69 NaN \n",
+ "1229 Degradation of EGFR in A431 cells after 16 h t... \n",
+ "\n",
+ " Article DOI \n",
+ "69 10.1016/j.ejmech.2020.112199 \n",
+ "1229 10.1016/j.ejmech.2020.112199 "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\\begin{tabular}{llllrrllll}\n",
+ "\\toprule\n",
+ "Name & Smiles & Cell Line Identifier & Active (Dmax 0.6, pDC50 6.0) & pDC50 & Dmax (\\%) & Uniprot & E3 Ligase & Assay (DC50/Dmax) & Article DOI \\\\\n",
+ "\\midrule\n",
+ " NaN & C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CCN... & H1975/WR & True & 8.229148 & 100.0 & P00533 & VHL & NaN & 10.1016/j.ejmech.2020.112199 \\\\\n",
+ " NaN & C=CC(=O)Nc1cccc(-n2c(=O)cc(C)c3cnc(Nc4ccc(N5CCN... & A431 siYAP & False & 5.698970 & NaN & P00533 & VHL & Degradation of EGFR in A431 cells after 16 h tr... & 10.1016/j.ejmech.2020.112199 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " NaN & CCC(=O)N[C@H]1CC[C@@H](n2c(=O)cc(C)c3cnc(Nc4ccc... & HCT 116 & False & 6.000000 & 28.0 & P33981 & CRBN & Degradation of TTK in COLO-205/HCT-116 cells af... & 10.1021/acs.jmedchem.1c01768 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
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+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " NaN & CCC(=O)N[C@H]1CC[C@@H](n2c(=O)cc(C)c3cnc(Nc4ccc... & COLO 205 & True & 7.503762 & 72.0 & P33981 & CRBN & Degradation of TTK in COLO-205/HCT-116 cells af... & 10.1021/acs.jmedchem.1c01768 \\\\\n",
+ " NaN & CCC(=O)N[C@H]1CC[C@@H](n2c(=O)cc(C)c3cnc(Nc4ccc... & HCT 116 & False & 6.000000 & 41.0 & P33981 & CRBN & Degradation of TTK in COLO-205/HCT-116 cells af... & 10.1021/acs.jmedchem.1c01768 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
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+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " NaN & CCC(=O)N[C@H]1CC[C@@H](n2c(=O)cc(C)c3cnc(Nc4ccc... & HCT 116 & False & 7.692504 & 50.0 & P33981 & CRBN & Degradation of TTK in COLO-205/HCT-116 cells af... & 10.1021/acs.jmedchem.1c01768 \\\\\n",
+ "\\bottomrule\n",
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+ ]
+ },
+ {
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+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " NaN & CCC(=O)N[C@H]1CC[C@@H](n2c(=O)cc(C)c3cnc(Nc4ccc... & HCT 116 & False & 6.793174 & 43.0 & P33981 & CRBN & Degradation of TTK in COLO-205/HCT-116 cells af... & 10.1021/acs.jmedchem.1c01768 \\\\\n",
+ "\\bottomrule\n",
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ "1562 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... SNU-423 \n",
+ "1563 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... HLF \n",
+ "1564 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... SNU-398 \n",
+ "1565 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... HuCC-T1-G10 \n",
+ "1566 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... HuH-1 \n",
+ "1567 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... HepG2 hALR \n",
+ "1568 COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@... SK-HEP-1 \n",
+ "\n",
+ " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n",
+ "1557 True 243.0 80.0 Q05397 VHL \n",
+ "1558 False 631.0 59.0 Q05397 VHL \n",
+ "1559 True 32.0 98.0 Q05397 VHL \n",
+ "1560 True 25.0 85.0 Q05397 VHL \n",
+ "1561 True 100.0 79.0 Q05397 VHL \n",
+ "1562 True 79.0 87.0 Q05397 VHL \n",
+ "1563 True 40.0 66.0 Q05397 VHL \n",
+ "1564 True 10.0 99.0 Q05397 VHL \n",
+ "1565 True 126.0 86.0 Q05397 VHL \n",
+ "1566 True 79.0 79.0 Q05397 VHL \n",
+ "1567 True 631.0 65.0 Q05397 VHL \n",
+ "1568 True 126.0 87.0 Q05397 VHL \n",
+ "\n",
+ " Assay (DC50/Dmax) \\\n",
+ "1557 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1558 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1559 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1560 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1561 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1562 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1563 Degradation of Fak in HLF/SNU-398/HUCCT1 cells... \n",
+ "1564 Degradation of Fak in HLF/SNU-398/HUCCT1 cells... \n",
+ "1565 Degradation of Fak in HLF/SNU-398/HUCCT1 cells... \n",
+ "1566 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "1567 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "1568 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "\n",
+ " Article DOI \n",
+ "1557 10.1021/acs.jmedchem.8b01826 \n",
+ "1558 10.1021/acs.jmedchem.8b01826 \n",
+ "1559 10.1021/acs.jmedchem.8b01826 \n",
+ "1560 10.1021/acs.jmedchem.8b01826 \n",
+ "1561 10.1021/acs.jmedchem.8b01826 \n",
+ "1562 10.1021/acs.jmedchem.8b01826 \n",
+ "1563 10.1021/acs.jmedchem.8b01826 \n",
+ "1564 10.1021/acs.jmedchem.8b01826 \n",
+ "1565 10.1021/acs.jmedchem.8b01826 \n",
+ "1566 10.1021/acs.jmedchem.8b01826 \n",
+ "1567 10.1021/acs.jmedchem.8b01826 \n",
+ "1568 10.1021/acs.jmedchem.8b01826 "
+ ]
+ },
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+ "output_type": "display_data"
+ },
+ {
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+ "output_type": "stream",
+ "text": [
+ "\\begin{tabular}{llllrrllll}\n",
+ "\\toprule\n",
+ " Name & Smiles & Cell Line Identifier & Active (Dmax 0.6, pDC50 6.0) & pDC50 & Dmax (\\%) & Uniprot & E3 Ligase & Assay (DC50/Dmax) & Article DOI \\\\\n",
+ "\\midrule\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & A549 Cas9 & True & 6.614394 & 80.0 & Q05397 & VHL & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & NaN & False & 6.199971 & 59.0 & Q05397 & VHL & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & SNU-387 & True & 7.494850 & 98.0 & Q05397 & VHL & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & HLE & True & 7.602060 & 85.0 & Q05397 & VHL & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & Huh-7 & True & 7.000000 & 79.0 & Q05397 & VHL & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & SNU-423 & True & 7.102373 & 87.0 & Q05397 & VHL & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & HLF & True & 7.397940 & 66.0 & Q05397 & VHL & Degradation of Fak in HLF/SNU-398/HUCCT1 cells ... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & SNU-398 & True & 8.000000 & 99.0 & Q05397 & VHL & Degradation of Fak in HLF/SNU-398/HUCCT1 cells ... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & HuCC-T1-G10 & True & 6.899629 & 86.0 & Q05397 & VHL & Degradation of Fak in HLF/SNU-398/HUCCT1 cells ... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & HuH-1 & True & 7.102373 & 79.0 & Q05397 & VHL & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & HepG2 hALR & True & 6.199971 & 65.0 & Q05397 & VHL & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-0319 & COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@H... & SK-HEP-1 & True & 6.899629 & 87.0 & Q05397 & VHL & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " Smiles Cell Line Identifier \\\n",
+ "1545 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... HLE \n",
+ "1546 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... Huh-7 \n",
+ "1547 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... SNU-423 \n",
+ "1548 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... HuH-1 \n",
+ "1549 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... HepG2 hALR \n",
+ "1550 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... SK-HEP-1 \n",
+ "1551 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... A549 Cas9 \n",
+ "1552 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... NaN \n",
+ "1553 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... SNU-387 \n",
+ "1555 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... SNU-398 \n",
+ "1556 COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(... HuCC-T1-G10 \n",
+ "\n",
+ " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n",
+ "1545 True 158.0 79.0 Q05397 CRBN \n",
+ "1546 True 50.0 93.0 Q05397 CRBN \n",
+ "1547 True 13.0 93.0 Q05397 CRBN \n",
+ "1548 False 251.0 50.0 Q05397 CRBN \n",
+ "1549 True 32.0 89.0 Q05397 CRBN \n",
+ "1550 True 32.0 89.0 Q05397 CRBN \n",
+ "1551 True 27.0 95.0 Q05397 CRBN \n",
+ "1552 True 13.0 96.0 Q05397 CRBN \n",
+ "1553 True 25.0 90.0 Q05397 CRBN \n",
+ "1555 True 3.0 95.0 Q05397 CRBN \n",
+ "1556 True 13.0 90.0 Q05397 CRBN \n",
+ "\n",
+ " Assay (DC50/Dmax) \\\n",
+ "1545 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1546 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1547 Degradation of Fak in HLE/HuH-7/SNU-423 cells ... \n",
+ "1548 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "1549 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "1550 Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cel... \n",
+ "1551 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1552 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1553 Degradation of Fak in A549/Hep3B2.1-7/SNU-387 ... \n",
+ "1555 Degradation of Fak in HLF/SNU-398/HUCCT1 cells... \n",
+ "1556 Degradation of Fak in HLF/SNU-398/HUCCT1 cells... \n",
+ "\n",
+ " Article DOI \n",
+ "1545 10.1021/acs.jmedchem.8b01826 \n",
+ "1546 10.1021/acs.jmedchem.8b01826 \n",
+ "1547 10.1021/acs.jmedchem.8b01826 \n",
+ "1548 10.1021/acs.jmedchem.8b01826 \n",
+ "1549 10.1021/acs.jmedchem.8b01826 \n",
+ "1550 10.1021/acs.jmedchem.8b01826 \n",
+ "1551 10.1021/acs.jmedchem.8b01826 \n",
+ "1552 10.1021/acs.jmedchem.8b01826 \n",
+ "1553 10.1021/acs.jmedchem.8b01826 \n",
+ "1555 10.1021/acs.jmedchem.8b01826 \n",
+ "1556 10.1021/acs.jmedchem.8b01826 "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\\begin{tabular}{llllrrllll}\n",
+ "\\toprule\n",
+ " Name & Smiles & Cell Line Identifier & Active (Dmax 0.6, pDC50 6.0) & pDC50 & Dmax (\\%) & Uniprot & E3 Ligase & Assay (DC50/Dmax) & Article DOI \\\\\n",
+ "\\midrule\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & HLE & True & 6.801343 & 79.0 & Q05397 & CRBN & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & Huh-7 & True & 7.301030 & 93.0 & Q05397 & CRBN & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & SNU-423 & True & 7.886057 & 93.0 & Q05397 & CRBN & Degradation of Fak in HLE/HuH-7/SNU-423 cells a... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & HuH-1 & False & 6.600326 & 50.0 & Q05397 & CRBN & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & HepG2 hALR & True & 7.494850 & 89.0 & Q05397 & CRBN & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & SK-HEP-1 & True & 7.494850 & 89.0 & Q05397 & CRBN & Degradation of Fak in HUH-1/HepG2/SK-Hep-1 cell... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & A549 Cas9 & True & 7.568636 & 95.0 & Q05397 & CRBN & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & NaN & True & 7.886057 & 96.0 & Q05397 & CRBN & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & SNU-387 & True & 7.602060 & 90.0 & Q05397 & CRBN & Degradation of Fak in A549/Hep3B2.1-7/SNU-387 c... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & SNU-398 & True & 8.522879 & 95.0 & Q05397 & CRBN & Degradation of Fak in HLF/SNU-398/HUCCT1 cells ... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "BI-3663 & COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(C... & HuCC-T1-G10 & True & 7.886057 & 90.0 & Q05397 & CRBN & Degradation of Fak in HLF/SNU-398/HUCCT1 cells ... & 10.1021/acs.jmedchem.8b01826 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ "1299 Degradation of SUZ12 in HeLa/DB cells after 24... \n",
+ "\n",
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+ "1296 10.1016/j.chembiol.2019.11.006 \n",
+ "1297 10.1016/j.chembiol.2019.11.006 \n",
+ "1298 10.1016/j.chembiol.2019.11.006 \n",
+ "1299 10.1016/j.chembiol.2019.11.006 "
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+ "\\begin{tabular}{llllrrllll}\n",
+ "\\toprule\n",
+ " Name & Smiles & Cell Line Identifier & Active (Dmax 0.6, pDC50 6.0) & pDC50 & Dmax (\\%) & Uniprot & E3 Ligase & Assay (DC50/Dmax) & Article DOI \\\\\n",
+ "\\midrule\n",
+ "UNC6852 & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & HeLa & True & 6.102373 & 92.0 & O75530 & VHL & Degradation of EED in HeLa/DB cells after 24 h ... & 10.1016/j.chembiol.2019.11.006 \\\\\n",
+ "UNC6852 & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & HeLa & True & 6.522879 & 75.0 & Q15910 & VHL & Degradation of EZH2 in HeLa/DB cells after 24 h... & 10.1016/j.chembiol.2019.11.006 \\\\\n",
+ "UNC6852 & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & DB & True & 6.173925 & 96.0 & Q15910 & VHL & Degradation of EZH2 in HeLa/DB cells after 24 h... & 10.1016/j.chembiol.2019.11.006 \\\\\n",
+ "UNC6852 & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & HeLa & False & NaN & 22.0 & Q15022 & VHL & Degradation of SUZ12 in HeLa/DB cells after 24 ... & 10.1016/j.chembiol.2019.11.006 \\\\\n",
+ "UNC6852 & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & DB & True & 6.229148 & 82.0 & Q15022 & VHL & Degradation of SUZ12 in HeLa/DB cells after 24 ... & 10.1016/j.chembiol.2019.11.006 \\\\\n",
+ "\\bottomrule\n",
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+ ]
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+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ " NaN & Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & VCaP & False & 7.30103 & 51.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells after 2-4... & 10.1021/acsmedchemlett.9b00115 \\\\\n",
+ "\\bottomrule\n",
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ "DT2216 & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & MOLT-4 & True & 7.200659 & 90.8 & Q07817 & VHL & Degradation of BCL-xL in MOLT-4/platelets cells... & 10.1038/s41591-019-0668-z \\\\\n",
+ "DT2216 & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & 2T60 & False & 5.522879 & 26.0 & Q07817 & VHL & Degradation of BCL-xL in MOLT-4/platelets cells... & 10.1038/s41591-019-0668-z \\\\\n",
+ "\\bottomrule\n",
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+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
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+ "\\midrule\n",
+ " NaN & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & LNCaP & True & 7.30103 & 71.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells using ELI... & 10.1021/acsmedchemlett.0c00236 \\\\\n",
+ " NaN & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & VCaP & False & 7.30103 & 51.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells using ELI... & 10.1021/acsmedchemlett.0c00236 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "\n",
+ "
\n",
+ " \n",
+ " \n",
+ " | \n",
+ " Smiles | \n",
+ " Cell Line Identifier | \n",
+ " Active (Dmax 0.6, pDC50 6.0) | \n",
+ " DC50 (nM) | \n",
+ " Dmax (%) | \n",
+ " Uniprot | \n",
+ " E3 Ligase | \n",
+ " Assay (DC50/Dmax) | \n",
+ " Article DOI | \n",
+ "
\n",
+ " \n",
+ " \n",
+ " \n",
+ " 1477 | \n",
+ " Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)... | \n",
+ " LNCaP | \n",
+ " True | \n",
+ " 50.0 | \n",
+ " 71.0 | \n",
+ " P10275 | \n",
+ " VHL | \n",
+ " Degradation of AR in LNCaP/VCaP cells using EL... | \n",
+ " 10.1021/acsmedchemlett.0c00236 | \n",
+ "
\n",
+ " \n",
+ " 1478 | \n",
+ " Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)... | \n",
+ " VCaP | \n",
+ " False | \n",
+ " 50.0 | \n",
+ " 51.0 | \n",
+ " P10275 | \n",
+ " VHL | \n",
+ " Degradation of AR in LNCaP/VCaP cells using EL... | \n",
+ " 10.1021/acsmedchemlett.0c00236 | \n",
+ "
\n",
+ " \n",
+ "
\n",
+ "
"
+ ],
+ "text/plain": [
+ " Smiles Cell Line Identifier \\\n",
+ "1477 Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)... LNCaP \n",
+ "1478 Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)... VCaP \n",
+ "\n",
+ " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n",
+ "1477 True 50.0 71.0 P10275 VHL \n",
+ "1478 False 50.0 51.0 P10275 VHL \n",
+ "\n",
+ " Assay (DC50/Dmax) \\\n",
+ "1477 Degradation of AR in LNCaP/VCaP cells using EL... \n",
+ "1478 Degradation of AR in LNCaP/VCaP cells using EL... \n",
+ "\n",
+ " Article DOI \n",
+ "1477 10.1021/acsmedchemlett.0c00236 \n",
+ "1478 10.1021/acsmedchemlett.0c00236 "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "\\begin{tabular}{llllrrllll}\n",
+ "\\toprule\n",
+ "Name & Smiles & Cell Line Identifier & Active (Dmax 0.6, pDC50 6.0) & pDC50 & Dmax (\\%) & Uniprot & E3 Ligase & Assay (DC50/Dmax) & Article DOI \\\\\n",
+ "\\midrule\n",
+ " NaN & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & LNCaP & True & 7.30103 & 71.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells using ELI... & 10.1021/acsmedchemlett.0c00236 \\\\\n",
+ " NaN & Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)C... & VCaP & False & 7.30103 & 51.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells using ELI... & 10.1021/acsmedchemlett.0c00236 \\\\\n",
+ "\\bottomrule\n",
+ "\\end{tabular}\n",
+ "\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/tmp/ipykernel_3711258/332080580.py:17: FutureWarning: In future versions `DataFrame.to_latex` is expected to utilise the base implementation of `Styler.to_latex` for formatting and rendering. The arguments signature may therefore change. It is recommended instead to use `DataFrame.style.to_latex` which also contains additional functionality.\n",
+ " print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n"
+ ]
+ }
+ ],
+ "source": [
+ "# Get the entries for which the same SMILES is active for one cell and inactive for another\n",
+ "# This is a sign of a potential error in the data\n",
+ "# This is a sign of a potential error in the data\n",
+ "active_smiles = train_val_df[train_val_df[active_col] == 1]['Smiles']\n",
+ "inactive_smiles = train_val_df[train_val_df[active_col] == 0]['Smiles']\n",
+ "active_smiles = active_smiles.drop_duplicates()\n",
+ "inactive_smiles = inactive_smiles.drop_duplicates()\n",
+ "\n",
+ "common_smiles = active_smiles[active_smiles.isin(inactive_smiles)]\n",
+ "common_df = train_val_df[train_val_df['Smiles'].isin(common_smiles)]\n",
+ "\n",
+ "# # Group by Smiles and check if the same SMILES is active for one cell and inactive for another\n",
+ "# grouped = common_df.groupby('Smiles')\n",
+ "# for name, group in grouped:\n",
+ "# if group[active_col].nunique() > 1 and group['Cell Line Identifier'].nunique() > 1:\n",
+ "# display(group[['Smiles', 'Cell Line Identifier', active_col, 'DC50 (nM)', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']])\n",
+ "# print(group[['Name', 'Smiles', 'Cell Line Identifier', active_col, 'pDC50', 'Dmax (%)', 'Uniprot', 'E3 Ligase', 'Assay (DC50/Dmax)', 'Article DOI']].to_latex(index=False))\n",
+ "# print()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
{
"cell_type": "code",
"execution_count": 29,
@@ -256,18 +2331,6 @@
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.10.8"
}
},
"nbformat": 4,