{"id":4506,"date":"2025-11-07T12:50:17","date_gmt":"2025-11-07T03:50:17","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=4506"},"modified":"2025-11-07T12:53:29","modified_gmt":"2025-11-07T03:53:29","slug":"drug-target-interaction-using-a-deep-learning-model","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/drug-target-interaction-using-a-deep-learning-model\/","title":{"rendered":"Drug Target Interaction using a deep learning model"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Introduction <\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A toy example for using a deep learning model to predict drug &#8211; target interaction <\/li>\n<\/ul>\n\n\n\n<p class=\"wp-block-paragraph\"><\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>required files <\/li>\n<\/ul>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-b3825af9-8926-4a47-8786-7d8b0f606dd6\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/map4k1.tsv\">map4k1<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/map4k1.tsv\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-b3825af9-8926-4a47-8786-7d8b0f606dd6\">Download<\/a><\/div>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-2d55aa9e-55f9-4f23-b42d-95df4ff1326e\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/cdk9.tsv\">cdk9<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/cdk9.tsv\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-2d55aa9e-55f9-4f23-b42d-95df4ff1326e\">Download<\/a><\/div>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-63988435-a0c7-4c57-80ff-be1580890b6d\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/rna_polymerase.tsv\">rna_polymerase<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/rna_polymerase.tsv\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-63988435-a0c7-4c57-80ff-be1580890b6d\">Download<\/a><\/div>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-bd284a37-e7e5-45f7-b7b1-e02f99fdf41a\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/antibiotics.tsv\">antibiotics<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2025\/11\/antibiotics.tsv\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-bd284a37-e7e5-45f7-b7b1-e02f99fdf41a\">Download<\/a><\/div>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">import pandas as pd\n\npositive_dataset = pd.read_csv('cdk9.tsv', sep='\\t', header=0, index_col=0) \nnegative_dataset = pd.read_csv('antibiotics.tsv', sep='\\t', header=0, index_col=0) \n\nprint(f'Number of positive dataset: {len(positive_dataset)}')\nprint(f'Number of negative dataset: {len(negative_dataset)}')<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">from rdkit.Chem import AllChem\nfrom rdkit.Chem.rdFingerprintGenerator import GetMorganGenerator\n\nimport numpy as np\n\nX = []\ny = []\n\n# positive dataset\nfor sm in positive_dataset['Smiles']: \n    if isinstance(sm, str):\n        m = AllChem.MolFromSmiles(sm)\n        gen = GetMorganGenerator(7, fpSize=1024)\n        fp = gen.GetFingerprint(m)\n        X.append(np.array(fp)) # molecular fingerprint\n        y.append(1)            # positive dataset\n\n# negative dataset\nfor sm in negative_dataset['Smiles']:\n    if isinstance(sm, str):\n        m = AllChem.MolFromSmiles(sm)\n        gen = GetMorganGenerator(7, fpSize=1024)\n        fp = gen.GetFingerprint(m)\n        X.append(np.array(fp)) # molecular fingerprint\n        y.append(0)            # negative dataset\n\nX = np.array(X)\ny = np.array(y)\n\nprint(f'Total number of chemicals: {len(X)}')\nprint(f'Number of positive dataset: {np.sum(y)}')\nprint(f'Number of negative dataset: {len(y) - np.sum(y)}')\nprint(f'Size of a fingerprint: {len(X[0])}')      <\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">import tensorflow as tf # Deep learning \ub77c\uc774\ube0c\ub7ec\ub9ac\n\nmodel = tf.keras.models.Sequential([\n    tf.keras.layers.Dense(1000, input_shape=(X.shape[1],), activation='relu'),\n    tf.keras.layers.Dense(1000, activation='relu'),   \n    tf.keras.layers.Dense(1000, activation='relu'),    \n    tf.keras.layers.Dense(1, activation='sigmoid')\n])\nmodel.summary()<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">model.compile(optimizer='SGD', loss='binary_crossentropy', metrics=['accuracy'])\n<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">history = model.fit(X, y, validation_split=0.1, epochs=50, verbose=0)<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">import matplotlib.pyplot as plt\n# \uadf8\ub9bc \uadf8\ub9b4 \uacf5\uac04 \uc900\ube44\nfig = plt.figure()         # \uadf8\ub9bc\uc744 \uadf8\ub9b4 \uc218 \uc788\ub294 \uacf5\uac04\uc744 \ub9cc\ub4e0\ub2e4\nax = fig.add_subplot(111)  # x\ucd95, y\ucd95\uc744 \uac00\uc9c4 \uacf5\uac04\uc744 \ub9cc\ub4e0\ub2e4\n\n# \uc8fc\uc694 \ub370\uc774\ud130 plot\ud558\uae30\nax.plot(history.history['accuracy'])      # train dataset\uc758 accuracy\ub97c plot\ud55c\ub2e4. \nax.plot(history.history['val_accuracy'])  # validation dataset\uc758 accuracy\ub97c plot\ud55c\ub2e4. \n\n# \uc124\uba85 \ucd94\uac00 \ub4f1 \uae30\ud0c0\nax.set_xlabel('epoch')              # x\ucd95 \uc774\ub984\uc744 \ud45c\uae30\ud55c\ub2e4.\nax.set_ylabel('accuracy')           # y\ucd95 \uc774\ub984\uc744 \ud45c\uae30\ud55c\ub2e4.\nax.grid()                           # Grid\ub97c \ud45c\uc2dc\ud558\uc5ec \ubcf4\uae30 \uc27d\uac8c \ud55c\ub2e4.\nax.set_ylim([-0.05, 1.05])          # y\ucd95 \uac12\uc758 \ubc94\uc704\ub97c \uc9c0\uc815\ud55c\ub2e4.\nax.legend(['train', 'validation'])  # \ubc94\ub840(legend)\ub97c \ucd94\uac00\ud55c\ub2e4<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">kinase_dataset = pd.read_csv('map4k1.tsv', sep='\\t', header=0, index_col=0) \nrp_dataset = pd.read_csv('rna_polymerase.tsv', sep='\\t', header=0, index_col=0) \nprint(f'Number of kinase dataset: {len(kinase_dataset)}')\nprint(f'Number of RNA polymerase dataset: {len(kinase_dataset)}')\n\nXk = []\nfor sm in kinase_dataset['Smiles']: \n    if isinstance(sm, str):\n        m = AllChem.MolFromSmiles(sm)\n        gen = GetMorganGenerator(7, fpSize=1024)\n        fp = gen.GetFingerprint(m)\n        Xk.append(np.array(fp)) # molecular fingerprint\nXk = np.array(Xk)\n\nXrp = []\nfor sm in rp_dataset['Smiles']: \n    if isinstance(sm, str):\n        m = AllChem.MolFromSmiles(sm)\n        gen = GetMorganGenerator(7, fpSize=1024)\n        fp = gen.GetFingerprint(m)\n        Xrp.append(np.array(fp)) # molecular fingerprint\nXrp = np.array(Xrp)<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">yk_pred = model.predict(Xk)\nyrp_pred = model.predict(Xrp)<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"python\" class=\"language-python\">fig = plt.figure()\nax = fig.add_subplot(111)\nax.hist(yk_pred, alpha=0.5, density=1, label='kinase')\nax.hist(yrp_pred, alpha=0.5, density=1, label='rna_polymerase')\nax.legend()\nax.grid()\nax.set_xlabel('Predictive value')\nax.set_ylabel('Density')<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>Introduction<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center 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