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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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1557COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...A549 Cas9True243.080.0Q05397VHLDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1558COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...NaNFalse631.059.0Q05397VHLDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1559COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...SNU-387True32.098.0Q05397VHLDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1560COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...HLETrue25.085.0Q05397VHLDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1561COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...Huh-7True100.079.0Q05397VHLDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1562COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...SNU-423True79.087.0Q05397VHLDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1563COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...HLFTrue40.066.0Q05397VHLDegradation of Fak in HLF/SNU-398/HUCCT1 cells...10.1021/acs.jmedchem.8b01826
1564COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...SNU-398True10.099.0Q05397VHLDegradation of Fak in HLF/SNU-398/HUCCT1 cells...10.1021/acs.jmedchem.8b01826
1565COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...HuCC-T1-G10True126.086.0Q05397VHLDegradation of Fak in HLF/SNU-398/HUCCT1 cells...10.1021/acs.jmedchem.8b01826
1566COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...HuH-1True79.079.0Q05397VHLDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
1567COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...HepG2 hALRTrue631.065.0Q05397VHLDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
1568COc1cc(C(=O)NCCOCCOCCOCC(=O)N[C@H](C(=O)N2C[C@...SK-HEP-1True126.087.0Q05397VHLDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
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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 " + ] + }, + "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-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" + ] + }, + { + "data": { + "text/html": [ + "
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1545COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...HLETrue158.079.0Q05397CRBNDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1546COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...Huh-7True50.093.0Q05397CRBNDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1547COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...SNU-423True13.093.0Q05397CRBNDegradation of Fak in HLE/HuH-7/SNU-423 cells ...10.1021/acs.jmedchem.8b01826
1548COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...HuH-1False251.050.0Q05397CRBNDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
1549COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...HepG2 hALRTrue32.089.0Q05397CRBNDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
1550COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...SK-HEP-1True32.089.0Q05397CRBNDegradation of Fak in HUH-1/HepG2/SK-Hep-1 cel...10.1021/acs.jmedchem.8b01826
1551COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...A549 Cas9True27.095.0Q05397CRBNDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1552COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...NaNTrue13.096.0Q05397CRBNDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1553COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...SNU-387True25.090.0Q05397CRBNDegradation of Fak in A549/Hep3B2.1-7/SNU-387 ...10.1021/acs.jmedchem.8b01826
1555COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...SNU-398True3.095.0Q05397CRBNDegradation of Fak in HLF/SNU-398/HUCCT1 cells...10.1021/acs.jmedchem.8b01826
1556COc1cc(C(=O)NCCOCCOCCOCCC(=O)Nc2cccc3c2C(=O)N(...HuCC-T1-G10True13.090.0Q05397CRBNDegradation of Fak in HLF/SNU-398/HUCCT1 cells...10.1021/acs.jmedchem.8b01826
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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" + ] + }, + { + "data": { + "text/html": [ + "
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1294Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...HeLaTrue790.092.0O75530VHLDegradation of EED in HeLa/DB cells after 24 h...10.1016/j.chembiol.2019.11.006
1296Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...HeLaTrue300.075.0Q15910VHLDegradation of EZH2 in HeLa/DB cells after 24 ...10.1016/j.chembiol.2019.11.006
1297Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...DBTrue670.096.0Q15910VHLDegradation of EZH2 in HeLa/DB cells after 24 ...10.1016/j.chembiol.2019.11.006
1298Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...HeLaFalseNaN22.0Q15022VHLDegradation of SUZ12 in HeLa/DB cells after 24...10.1016/j.chembiol.2019.11.006
1299Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...DBTrue590.082.0Q15022VHLDegradation of SUZ12 in HeLa/DB cells after 24...10.1016/j.chembiol.2019.11.006
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" + ], + "text/plain": [ + " Smiles Cell Line Identifier \\\n", + "1294 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... HeLa \n", + "1296 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... HeLa \n", + "1297 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... DB \n", + "1298 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... HeLa \n", + "1299 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... DB \n", + "\n", + " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n", + "1294 True 790.0 92.0 O75530 VHL \n", + "1296 True 300.0 75.0 Q15910 VHL \n", + "1297 True 670.0 96.0 Q15910 VHL \n", + "1298 False NaN 22.0 Q15022 VHL \n", + "1299 True 590.0 82.0 Q15022 VHL \n", + "\n", + " Assay (DC50/Dmax) \\\n", + "1294 Degradation of EED in HeLa/DB cells after 24 h... \n", + "1296 Degradation of EZH2 in HeLa/DB cells after 24 ... \n", + "1297 Degradation of EZH2 in HeLa/DB cells after 24 ... \n", + "1298 Degradation of SUZ12 in HeLa/DB cells after 24... \n", + "1299 Degradation of SUZ12 in HeLa/DB cells after 24... \n", + "\n", + " Article DOI \n", + "1294 10.1016/j.chembiol.2019.11.006 \n", + "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 " + ] + }, + "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", + "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", + "\\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": [ + "
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1435Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...LNCaPTrue50.071.0P10275VHLDegradation of AR in LNCaP/VCaP cells after 2-...10.1021/acsmedchemlett.9b00115
1436Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O...VCaPFalse50.051.0P10275VHLDegradation of AR in LNCaP/VCaP cells after 2-...10.1021/acsmedchemlett.9b00115
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" + ], + "text/plain": [ + " Smiles Cell Line Identifier \\\n", + "1435 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... LNCaP \n", + "1436 Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O... VCaP \n", + "\n", + " Active (Dmax 0.6, pDC50 6.0) DC50 (nM) Dmax (%) Uniprot E3 Ligase \\\n", + "1435 True 50.0 71.0 P10275 VHL \n", + "1436 False 50.0 51.0 P10275 VHL \n", + "\n", + " Assay (DC50/Dmax) \\\n", + "1435 Degradation of AR in LNCaP/VCaP cells after 2-... \n", + "1436 Degradation of AR in LNCaP/VCaP cells after 2-... \n", + "\n", + " Article DOI \n", + "1435 10.1021/acsmedchemlett.9b00115 \n", + "1436 10.1021/acsmedchemlett.9b00115 " + ] + }, + "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(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)... & LNCaP & True & 7.30103 & 71.0 & P10275 & VHL & Degradation of AR in LNCaP/VCaP cells after 2-4... & 10.1021/acsmedchemlett.9b00115 \\\\\n", + " 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", + "\\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": [ + "
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
4Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...MOLT-4True53.0100.0Q07817VHLNaN10.1016/j.ejmech.2020.112186
1245Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...MOLT-4True63.090.8Q07817VHLDegradation of BCL-xL in MOLT-4/platelets cell...10.1038/s41591-019-0668-z
1246Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...2T60False3000.026.0Q07817VHLDegradation of BCL-xL in MOLT-4/platelets cell...10.1038/s41591-019-0668-z
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1479Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...LNCaPTrue50.071.0P10275VHLDegradation of AR in LNCaP/VCaP cells using EL...10.1021/acsmedchemlett.0c00236
1480Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...VCaPFalse50.051.0P10275VHLDegradation of AR in LNCaP/VCaP cells using EL...10.1021/acsmedchemlett.0c00236
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" + ], + "text/plain": [ + " Smiles Cell Line Identifier \\\n", + "1479 Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)... LNCaP \n", + "1480 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", + "1479 True 50.0 71.0 P10275 VHL \n", + "1480 False 50.0 51.0 P10275 VHL \n", + "\n", + " Assay (DC50/Dmax) \\\n", + "1479 Degradation of AR in LNCaP/VCaP cells using EL... \n", + "1480 Degradation of AR in LNCaP/VCaP cells using EL... \n", + "\n", + " Article DOI \n", + "1479 10.1021/acsmedchemlett.0c00236 \n", + "1480 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" + ] + }, + { + "data": { + "text/html": [ + "
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SmilesCell Line IdentifierActive (Dmax 0.6, pDC50 6.0)DC50 (nM)Dmax (%)UniprotE3 LigaseAssay (DC50/Dmax)Article DOI
1477Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...LNCaPTrue50.071.0P10275VHLDegradation of AR in LNCaP/VCaP cells using EL...10.1021/acsmedchemlett.0c00236
1478Cc1ncsc1-c1ccc([C@H](C)NC(=O)[C@@H]2C[C@@H](O)...VCaPFalse50.051.0P10275VHLDegradation of AR in LNCaP/VCaP cells using EL...10.1021/acsmedchemlett.0c00236
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" + ], + "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,