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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "ee43bf48-5491-4dc4-aa09-cb4a0f460f97",
"metadata": {},
"outputs": [],
"source": [
"from openbabel import pybel\n",
"from Bio.PDB import * \n"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "26bc18a2-a6eb-49d3-be80-876ddc7dd8e1",
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "3b59cfb4-c42a-425d-9653-44f07f9e864e",
"metadata": {},
"outputs": [],
"source": [
"df = pd.read_table('biolip/data/BioLiP_2013-03-6_nr.txt',sep='\\t',header=None,usecols=[0,4,5,6,13,14,15,16,19])\n",
"df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain',\n",
" 13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb',\n",
" 19: 'seq'})"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "01123edd-2b98-4fcc-a2e9-28213b9bed82",
"metadata": {},
"outputs": [],
"source": [
"base = 'biolip/data/ligand_nr/'\n",
"df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb'"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "bd8671da-66ad-40ad-b221-e33228be65f4",
"metadata": {},
"outputs": [],
"source": [
"df_complex = pd.read_parquet('data/biolip_complex.parquet')"
]
},
{
"cell_type": "code",
"execution_count": 97,
"id": "08b04d75-c01e-4b26-ae2d-622efae3bd1f",
"metadata": {},
"outputs": [],
"source": [
"df_affinity = df_complex[~df_complex['affinity_lit'].isnull() | ~df_complex['affinity_moad'].isnull() \n",
" | ~df_complex['affinity_pdbbind-cn'].isnull() | ~df_complex['affinity_bindingdb'].isnull()].copy()"
]
},
{
"cell_type": "code",
"execution_count": 98,
"id": "97af5533-10fe-4419-a998-ed80b7d26690",
"metadata": {},
"outputs": [],
"source": [
"from pint import UnitRegistry\n",
"import numpy as np\n",
"import re\n",
"ureg = UnitRegistry()\n",
"\n",
"def to_uM(affinities):\n",
" lit, moad, pdbbind, bindingdb = affinities\n",
"\n",
" vals = []\n",
" try:\n",
" lit = re.split('[=~<>]',str(lit))[1].split(' ')[0]\n",
" lit = ureg(lit).m_as(ureg.uM)\n",
" vals.append(lit)\n",
" except:\n",
" pass\n",
"\n",
" try:\n",
" moad = re.split('[=~<>]',str(moad))[1].split(' ')[0]\n",
" moad = ureg(moad).m_as(ureg.uM)\n",
" vals.append(moad)\n",
" except:\n",
" pass\n",
"\n",
" try:\n",
" pdbbind = re.split('[=~<>]',str(pdbbind))[1].split(' ')[0]\n",
" pdbbind = ureg(bindingdb).m_as(ureg.uM)\n",
" vals.append(pdbbind)\n",
" except:\n",
" pass\n",
"\n",
" try:\n",
" bindingdb = re.split('[=~<>]',str(bindingdb))[1].split(' ')[0]\n",
" bindingdb = ureg(bindingdb).m_as(ureg.uM)\n",
" vals.append(bindingdb)\n",
" except:\n",
" pass\n",
"\n",
" if len(vals) > 0:\n",
" vals = np.array(vals)\n",
" return np.mean(vals[~np.isnan(vals)])\n",
" \n",
" return None"
]
},
{
"cell_type": "code",
"execution_count": 99,
"id": "e21154a9-d3a0-4aa3-986f-cfeebc280da6",
"metadata": {},
"outputs": [],
"source": [
"df_affinity['affinity_uM'] = df_affinity[['affinity_lit','affinity_moad','affinity_pdbbind-cn','affinity_bindingdb']].apply(to_uM,axis=1)"
]
},
{
"cell_type": "code",
"execution_count": 101,
"id": "0fc94de0-823d-4f4f-9904-1c4d1e722c2e",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>pdb</th>\n",
" <th>chain</th>\n",
" <th>l_id</th>\n",
" <th>l_chain</th>\n",
" <th>affinity_lit</th>\n",
" <th>affinity_moad</th>\n",
" <th>affinity_pdbbind-cn</th>\n",
" <th>affinity_bindingdb</th>\n",
" <th>seq</th>\n",
" <th>ligand_fn</th>\n",
" <th>smiles</th>\n",
" <th>affinity_uM</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>38</th>\n",
" <td>11gs</td>\n",
" <td>EAA</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>ki=1.5uM (GTT EAA)</td>\n",
" <td>Ki=1.5uM (GTT-EAA)</td>\n",
" <td>None</td>\n",
" <td>PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC...</td>\n",
" <td>biolip/data/ligand_nr/11gs_EAA_A_1.pdb</td>\n",
" <td>CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C</td>\n",
" <td>1.500</td>\n",
" </tr>\n",
" <tr>\n",
" <th>43</th>\n",
" <td>13gs</td>\n",
" <td>SAS</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>ki=24uM (SAS)</td>\n",
" <td>Ki=24uM (SAS)</td>\n",
" <td>None</td>\n",
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
" <td>biolip/data/ligand_nr/13gs_SAS_A_1.pdb</td>\n",
" <td>OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c...</td>\n",
" <td>24.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>54</th>\n",
" <td>17gs</td>\n",
" <td>GTX</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>Kd=10000nM</td>\n",
" <td>MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA...</td>\n",
" <td>biolip/data/ligand_nr/17gs_GTX_A_1.pdb</td>\n",
" <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",
" <td>10.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>55</th>\n",
" <td>181l</td>\n",
" <td>BNZ</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>Ka=5700M^-1 (BNZ)</td>\n",
" <td>None</td>\n",
" <td>Kd=175000nM</td>\n",
" <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
" <td>biolip/data/ligand_nr/181l_BNZ_A_1.pdb</td>\n",
" <td>c1ccccc1</td>\n",
" <td>175.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>56</th>\n",
" <td>182l</td>\n",
" <td>BZF</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>Ka=8900M^-1 (BZF)</td>\n",
" <td>None</td>\n",
" <td>Kd=112000nM</td>\n",
" <td>MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL...</td>\n",
" <td>biolip/data/ligand_nr/182l_BZF_A_1.pdb</td>\n",
" <td>c1ccc2c(c1)occ2</td>\n",
" <td>112.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>...</th>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" <td>...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>105087</th>\n",
" <td>8kme</td>\n",
" <td>III</td>\n",
" <td>3</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>ki=8uM (BNN CUC TRG LEU PRO)</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
" <td>biolip/data/ligand_nr/8kme_III_3_1.pdb</td>\n",
" <td>O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(...</td>\n",
" <td>8.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>105088</th>\n",
" <td>8kme</td>\n",
" <td>III</td>\n",
" <td>4</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>ki=8uM (BNN CUC TRG LEU PRO)</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL...</td>\n",
" <td>biolip/data/ligand_nr/8kme_III_4_1.pdb</td>\n",
" <td>CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H...</td>\n",
" <td>8.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>105106</th>\n",
" <td>966c</td>\n",
" <td>RS2</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>ki=23nM (RS2)</td>\n",
" <td>Ki=23nM (RS2)</td>\n",
" <td>None</td>\n",
" <td>RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS...</td>\n",
" <td>biolip/data/ligand_nr/966c_RS2_A_1.pdb</td>\n",
" <td>ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1</td>\n",
" <td>0.023</td>\n",
" </tr>\n",
" <tr>\n",
" <th>105124</th>\n",
" <td>9icd</td>\n",
" <td>NAP</td>\n",
" <td>A</td>\n",
" <td>1</td>\n",
" <td>None</td>\n",
" <td>kd=125uM (NAP)</td>\n",
" <td>Kd=125uM (NAP)</td>\n",
" <td>None</td>\n",
" <td>SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV...</td>\n",
" <td>biolip/data/ligand_nr/9icd_NAP_A_1.pdb</td>\n",
" <td>O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O...</td>\n",
" <td>125.000</td>\n",
" </tr>\n",
" <tr>\n",
" <th>105138</th>\n",
" <td>9nse</td>\n",
" <td>ISU</td>\n",
" <td>B</td>\n",
" <td>2</td>\n",
" <td>None</td>\n",
" <td>Ki=0.039uM (ISU)</td>\n",
" <td>None</td>\n",
" <td>None</td>\n",
" <td>KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR...</td>\n",
" <td>biolip/data/ligand_nr/9nse_ISU_B_2.pdb</td>\n",
" <td>CC[Se]C(=N)N</td>\n",
" <td>0.039</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>7588 rows × 12 columns</p>\n",
"</div>"
],
"text/plain": [
" pdb chain l_id l_chain affinity_lit affinity_moad \\\n",
"38 11gs EAA A 1 None ki=1.5uM (GTT EAA) \n",
"43 13gs SAS A 1 None ki=24uM (SAS) \n",
"54 17gs GTX A 1 None None \n",
"55 181l BNZ A 1 None Ka=5700M^-1 (BNZ) \n",
"56 182l BZF A 1 None Ka=8900M^-1 (BZF) \n",
"... ... ... ... ... ... ... \n",
"105087 8kme III 3 1 None ki=8uM (BNN CUC TRG LEU PRO) \n",
"105088 8kme III 4 1 None ki=8uM (BNN CUC TRG LEU PRO) \n",
"105106 966c RS2 A 1 None ki=23nM (RS2) \n",
"105124 9icd NAP A 1 None kd=125uM (NAP) \n",
"105138 9nse ISU B 2 None Ki=0.039uM (ISU) \n",
"\n",
" affinity_pdbbind-cn affinity_bindingdb \\\n",
"38 Ki=1.5uM (GTT-EAA) None \n",
"43 Ki=24uM (SAS) None \n",
"54 None Kd=10000nM \n",
"55 None Kd=175000nM \n",
"56 None Kd=112000nM \n",
"... ... ... \n",
"105087 None None \n",
"105088 None None \n",
"105106 Ki=23nM (RS2) None \n",
"105124 Kd=125uM (NAP) None \n",
"105138 None None \n",
"\n",
" seq \\\n",
"38 PYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKASC... \n",
"43 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
"54 MPPYTVVYFPVRGRCAALRMLLADQGQSWKEEVVTVETWQEGSLKA... \n",
"55 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL... \n",
"56 MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSEL... \n",
"... ... \n",
"105087 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
"105088 IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLL... \n",
"105106 RWEQTHLTYRIENYTPDLPRADVDHAIEKAFQLWSNVTPLTFTKVS... \n",
"105124 SKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKV... \n",
"105138 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRKLQTR... \n",
"\n",
" ligand_fn \\\n",
"38 biolip/data/ligand_nr/11gs_EAA_A_1.pdb \n",
"43 biolip/data/ligand_nr/13gs_SAS_A_1.pdb \n",
"54 biolip/data/ligand_nr/17gs_GTX_A_1.pdb \n",
"55 biolip/data/ligand_nr/181l_BNZ_A_1.pdb \n",
"56 biolip/data/ligand_nr/182l_BZF_A_1.pdb \n",
"... ... \n",
"105087 biolip/data/ligand_nr/8kme_III_3_1.pdb \n",
"105088 biolip/data/ligand_nr/8kme_III_4_1.pdb \n",
"105106 biolip/data/ligand_nr/966c_RS2_A_1.pdb \n",
"105124 biolip/data/ligand_nr/9icd_NAP_A_1.pdb \n",
"105138 biolip/data/ligand_nr/9nse_ISU_B_2.pdb \n",
"\n",
" smiles affinity_uM \n",
"38 CC[C@H](C(=O)c1ccc(c(c1Cl)Cl)OCC(=O)O)C 1.500 \n",
"43 OC(=O)c1cc(/N=N/c2ccc(cc2)S(=O)(=O)Nc2ccccn2)c... 24.000 \n",
"54 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 10.000 \n",
"55 c1ccccc1 175.000 \n",
"56 c1ccc2c(c1)occ2 112.000 \n",
"... ... ... \n",
"105087 O=C[C@@H](NC(=O)[C@H](Cc1ccc(cc1)OS(O)(O)O)NC(... 8.000 \n",
"105088 CC(C[C@@H](C(=O)N1C=CC[C@H]1C(=O)N)NC(=O)[C@@H... 8.000 \n",
"105106 ONC(=O)CC1(CCOCC1)S(=O)(=O)c1ccc(cc1)Oc1ccccc1 0.023 \n",
"105124 O[C@@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@@H]1OP(=O... 125.000 \n",
"105138 CC[Se]C(=N)N 0.039 \n",
"\n",
"[7588 rows x 12 columns]"
]
},
"execution_count": 101,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df_affinity[~df_affinity['affinity_uM'].isnull()]"
]
},
{
"cell_type": "code",
"execution_count": 102,
"id": "2b483565-3c99-4c42-b2a9-f7b97cd8e80e",
"metadata": {},
"outputs": [],
"source": [
"df_affinity.to_parquet('data/biolip.parquet')"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "68dd5e45-b31d-492d-a47e-39072b67fa72",
"metadata": {},
"outputs": [],
"source": []
}
],
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|