jglaser/binding_affinity
A dataset to fine-tune language models on protein-ligand binding affinity prediction.
211.8k
1{2 "cells": [3 {4 "cell_type": "markdown",5 "id": "834aeced-c3c5-42a0-bad1-41e009dd86ee",6 "metadata": {},7 "source": [8 "### Preprocessing"9 ]10 },11 {12 "cell_type": "code",13 "execution_count": 1,14 "id": "86476f6e-802a-463b-a1b0-2ae228bb92af",15 "metadata": {},16 "outputs": [],17 "source": [18 "import pandas as pd"19 ]20 },21 {22 "cell_type": "code",23 "execution_count": 12,24 "id": "9b2be11c-f4bb-4107-af49-abd78052afcf",25 "metadata": {},26 "outputs": [],27 "source": [28 "df = pd.read_table('pdbbind/data/index/INDEX_general_PL_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",29 "df = df.rename(columns={'#': 'name','release': 'affinity'})\n",30 "df_refined = pd.read_table('pdbbind/data/index/INDEX_refined_data.2020',skiprows=4,sep=r'\\s+',usecols=[0,4]).drop(0)\n",31 "df_refined = df_refined.rename(columns={'#': 'name','release': 'affinity'})\n",32 "df = pd.concat([df,df_refined])"33 ]34 },35 {36 "cell_type": "code",37 "execution_count": 13,38 "id": "68983ab8-bf11-4ed6-ba06-f962dbdc077e",39 "metadata": {},40 "outputs": [],41 "source": [42 "quantities = ['ki','kd','ka','k1/2','kb','ic50','ec50']"43 ]44 },45 {46 "cell_type": "code",47 "execution_count": 14,48 "id": "3acbca3c-9c0b-43a1-a45e-331bf153bcfa",49 "metadata": {},50 "outputs": [],51 "source": [52 "from pint import UnitRegistry\n",53 "ureg = UnitRegistry()\n",54 "\n",55 "def to_uM(affinity):\n",56 " val = ureg(affinity)\n",57 " try:\n",58 " return val.m_as(ureg.uM)\n",59 " except Exception:\n",60 " pass\n",61 " \n",62 " try:\n",63 " return 1/val.m_as(1/ureg.uM)\n",64 " except Exception:\n",65 " pass"66 ]67 },68 {69 "cell_type": "code",70 "execution_count": 15,71 "id": "58e5748b-2cea-43ff-ab51-85a5021bd50b",72 "metadata": {},73 "outputs": [],74 "source": [75 "df['affinity_uM'] = df['affinity'].str.split('[=\\~><]').str[1].apply(to_uM)\n",76 "df['affinity_quantity'] = df['affinity'].str.split('[=\\~><]').str[0]"77 ]78 },79 {80 "cell_type": "code",81 "execution_count": 16,82 "id": "d92f0004-68c1-4487-94b9-56b4fd598de4",83 "metadata": {},84 "outputs": [85 {86 "data": {87 "text/plain": [88 "<AxesSubplot:>"89 ]90 },91 "execution_count": 16,92 "metadata": {},93 "output_type": "execute_result"94 },95 {96 "data": {97 "image/png": 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\n",98 "text/plain": [99 "<Figure size 432x288 with 1 Axes>"100 ]101 },102 "metadata": {103 "needs_background": "light"104 },105 "output_type": "display_data"106 }107 ],108 "source": [109 "df['affinity_quantity'].hist()"110 ]111 },112 {113 "cell_type": "code",114 "execution_count": 17,115 "id": "aa358835-55f3-4551-9217-e76a15de4fe8",116 "metadata": {},117 "outputs": [],118 "source": [119 "df_filter = df[df['affinity_quantity'].str.lower().isin(quantities)]"120 ]121 },122 {123 "cell_type": "code",124 "execution_count": 18,125 "id": "d6dda488-f709-4fe7-b372-080042cf7c66",126 "metadata": {},127 "outputs": [],128 "source": [129 "df_complex = pd.read_parquet('data/pdbbind_complex.parquet')"130 ]131 },132 {133 "cell_type": "code",134 "execution_count": 20,135 "id": "df7929e3-c7fd-4e1b-a165-92f8d53b9011",136 "metadata": {},137 "outputs": [],138 "source": [139 "df_all = df_complex.merge(df_filter,on='name').drop('affinity',axis=1)"140 ]141 },142 {143 "cell_type": "code",144 "execution_count": 21,145 "id": "41711825-b110-472b-a9f3-2eccc5afbfd9",146 "metadata": {},147 "outputs": [148 {149 "data": {150 "text/html": [151 "<div>\n",152 "<style scoped>\n",153 " .dataframe tbody tr th:only-of-type {\n",154 " vertical-align: middle;\n",155 " }\n",156 "\n",157 " .dataframe tbody tr th {\n",158 " vertical-align: top;\n",159 " }\n",160 "\n",161 " .dataframe thead th {\n",162 " text-align: right;\n",163 " }\n",164 "</style>\n",165 "<table border=\"1\" class=\"dataframe\">\n",166 " <thead>\n",167 " <tr style=\"text-align: right;\">\n",168 " <th></th>\n",169 " <th>name</th>\n",170 " <th>seq</th>\n",171 " <th>smiles</th>\n",172 " <th>affinity_uM</th>\n",173 " <th>affinity_quantity</th>\n",174 " </tr>\n",175 " </thead>\n",176 " <tbody>\n",177 " <tr>\n",178 " <th>0</th>\n",179 " <td>2lbv</td>\n",180 " <td>MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE...</td>\n",181 " <td>CCCCCCCCCCCCCCCCCCCC(=O)O</td>\n",182 " <td>0.02600</td>\n",183 " <td>Kd</td>\n",184 " </tr>\n",185 " <tr>\n",186 " <th>1</th>\n",187 " <td>1lt6</td>\n",188 " <td>APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE...</td>\n",189 " <td>OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]...</td>\n",190 " <td>500.00000</td>\n",191 " <td>IC50</td>\n",192 " </tr>\n",193 " <tr>\n",194 " <th>2</th>\n",195 " <td>4lwi</td>\n",196 " <td>VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE...</td>\n",197 " <td>COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)...</td>\n",198 " <td>0.02300</td>\n",199 " <td>IC50</td>\n",200 " </tr>\n",201 " <tr>\n",202 " <th>3</th>\n",203 " <td>3t4p</td>\n",204 " <td>AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM...</td>\n",205 " <td>OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)...</td>\n",206 " <td>6.43000</td>\n",207 " <td>Kd</td>\n",208 " </tr>\n",209 " <tr>\n",210 " <th>4</th>\n",211 " <td>6oyz</td>\n",212 " <td>YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL...</td>\n",213 " <td>CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1...</td>\n",214 " <td>0.18500</td>\n",215 " <td>IC50</td>\n",216 " </tr>\n",217 " <tr>\n",218 " <th>...</th>\n",219 " <td>...</td>\n",220 " <td>...</td>\n",221 " <td>...</td>\n",222 " <td>...</td>\n",223 " <td>...</td>\n",224 " </tr>\n",225 " <tr>\n",226 " <th>24754</th>\n",227 " <td>4j46</td>\n",228 " <td>GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD...</td>\n",229 " <td>CC[C@@H]([C@@H](C(=O)O)NC(=O)[C@@H]1CCCN1C(=O)...</td>\n",230 " <td>5.24000</td>\n",231 " <td>Ki</td>\n",232 " </tr>\n",233 " <tr>\n",234 " <th>24755</th>\n",235 " <td>2c80</td>\n",236 " <td>DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...</td>\n",237 " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",238 " <td>4.70000</td>\n",239 " <td>Kd</td>\n",240 " </tr>\n",241 " <tr>\n",242 " <th>24756</th>\n",243 " <td>2c80</td>\n",244 " <td>DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP...</td>\n",245 " <td>CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(...</td>\n",246 " <td>4.70000</td>\n",247 " <td>Kd</td>\n",248 " </tr>\n",249 " <tr>\n",250 " <th>24757</th>\n",251 " <td>5wl0</td>\n",252 " <td>NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI...</td>\n",253 " <td>OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)...</td>\n",254 " <td>0.00067</td>\n",255 " <td>Kd</td>\n",256 " </tr>\n",257 " <tr>\n",258 " <th>24758</th>\n",259 " <td>5wl0</td>\n",260 " <td>NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI...</td>\n",261 " <td>OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)...</td>\n",262 " <td>0.00067</td>\n",263 " <td>Kd</td>\n",264 " </tr>\n",265 " </tbody>\n",266 "</table>\n",267 "<p>24759 rows × 5 columns</p>\n",268 "</div>"269 ],270 "text/plain": [271 " name seq \\\n",272 "0 2lbv MTVPDRSEIAGKWYVVALASNTEFFLREKDKMKMAMARISFLGEDE... \n",273 "1 1lt6 APQTITELCSEYRNTQIYTINDKILSYTESMAGKREMVIITFKSGE... \n",274 "2 4lwi VETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYE... \n",275 "3 3t4p AAPFDKSKNVAQSIDQLIGQTPALYLNKLNNTKAKVVLKMECENPM... \n",276 "4 6oyz YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVIL... \n",277 "... ... ... \n",278 "24754 4j46 GTIYPRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGD... \n",279 "24755 2c80 DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP... \n",280 "24756 2c80 DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIP... \n",281 "24757 5wl0 NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI... \n",282 "24758 5wl0 NDDIDQSLIIAARNIVRRASVSADPLASLLEMCHSTQIGGTRMVDI... \n",283 "\n",284 " smiles affinity_uM \\\n",285 "0 CCCCCCCCCCCCCCCCCCCC(=O)O 0.02600 \n",286 "1 OC[C@H]1O[C@H](Oc2cccc(c2)N(=O)=O)[C@@H]([C@H]... 500.00000 \n",287 "2 COc1ccc(cc1)c1c(onc1c1cc(C(C)C)c(cc1O)O)NC(=O)... 0.02300 \n",288 "3 OC[C@@H](C(=O)N[C@@H]([C@H](CC)C)C(=O)O)NC(=O)... 6.43000 \n",289 "4 CO[C@@H]1[C@H](O[C@H]([C@@H]1O)n1ccc(=O)[nH]c1... 0.18500 \n",290 "... ... ... \n",291 "24754 CC[C@@H]([C@@H](C(=O)O)NC(=O)[C@@H]1CCCN1C(=O)... 5.24000 \n",292 "24755 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 4.70000 \n",293 "24756 CCCCCCSC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(... 4.70000 \n",294 "24757 OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)... 0.00067 \n",295 "24758 OC(=O)[C@H]1[C@@H]2CC[C@H]([C@@H]1Nc1nc(ncc1F)... 0.00067 \n",296 "\n",297 " affinity_quantity \n",298 "0 Kd \n",299 "1 IC50 \n",300 "2 IC50 \n",301 "3 Kd \n",302 "4 IC50 \n",303 "... ... \n",304 "24754 Ki \n",305 "24755 Kd \n",306 "24756 Kd \n",307 "24757 Kd \n",308 "24758 Kd \n",309 "\n",310 "[24759 rows x 5 columns]"311 ]312 },313 "execution_count": 21,314 "metadata": {},315 "output_type": "execute_result"316 }317 ],318 "source": [319 "df_all"320 ]321 },322 {323 "cell_type": "code",324 "execution_count": 53,325 "id": "4d105c42-0d11-49db-9012-52fafc9cd299",326 "metadata": {},327 "outputs": [],328 "source": [329 "df_all.to_parquet('data/pdbbind.parquet')"330 ]331 },332 {333 "cell_type": "code",334 "execution_count": 54,335 "id": "2955b056-26dd-45fa-8d74-f17661253a9a",336 "metadata": {},337 "outputs": [338 {339 "data": {340 "text/plain": [341 "24759"342 ]343 },344 "execution_count": 54,345 "metadata": {},346 "output_type": "execute_result"347 }348 ],349 "source": [350 "len(df_all)"351 ]352 },353 {354 "cell_type": "code",355 "execution_count": null,356 "id": "ed3fe035-6035-4d39-b072-d12dc0a95857",357 "metadata": {},358 "outputs": [],359 "source": []360 }361 ],362 "metadata": {363 "kernelspec": {364 "display_name": "Python 3",365 "language": "python",366 "name": "python3"367 },368 "language_info": {369 "codemirror_mode": {370 "name": "ipython",371 "version": 3372 },373 "file_extension": ".py",374 "mimetype": "text/x-python",375 "name": "python",376 "nbconvert_exporter": "python",377 "pygments_lexer": "ipython3",378 "version": "3.9.4"379 }380 },381 "nbformat": 4,382 "nbformat_minor": 5383}384