{"id":2778,"date":"2025-09-16T22:36:16","date_gmt":"2025-09-16T13:36:16","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=2778"},"modified":"2025-09-25T17:51:26","modified_gmt":"2025-09-25T08:51:26","slug":"core_embed_docking","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2025\/09\/16\/core_embed_docking\/","title":{"rendered":"\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u306e\u56fa\u5b9a\u3068\u30c9\u30c3\u30ad\u30f3\u30b0"},"content":{"rendered":"\n<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u5409\u68ee\u3067\u3059\u3002<br>\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u591a\u304f\u306f\u3001\u74b0\u69cb\u9020\u306b\u304a\u3051\u308b\u30a4\u30b9\u5f62\u3068\u821f\u5f62\u306a\u3069\u306e\u5909\u5316\u3092\u8003\u616e\u3067\u304d\u306a\u3044\u305f\u3081\u3001\u521d\u671f\u914d\u5ea7\u304c\u30c9\u30c3\u30ad\u30f3\u30b0\u306e\u7d50\u679c\u306b\u4e0e\u3048\u308b\u5f71\u97ff\u304c\u5927\u304d\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u4eca\u56de\u306f\u3001\u307e\u305a\u306f\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u56fa\u5b9a\u3057\u305f\u72b6\u614b\u3067\u5074\u9396\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u751f\u6210\u3055\u305b\u3001\u5206\u5b50\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u751f\u6210\u3057\u307e\u3059\u3002\u6b21\u306b\u3001\u305d\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u7528\u3044\u3066\u30c9\u30c3\u30ad\u30f3\u30b0\u3092\u884c\u3044\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u56fa\u5b9a\u3057\u305f\u521d\u671f\u914d\u5ea7\u306e\u751f\u6210<\/h3>\n\n\n\n<p>\u4e0b\u56f3\u306fXIAP\u3068\u963b\u5bb3\u5264\u306e\u7d50\u6676\u69cb\u9020(PDB:5OQW)\u3067\u3059\u304c\u3001\u9aa8\u683c\uff08\u70ad\u7d20\uff1a\u7070\u8272\uff09\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u56fa\u5b9a\u3057\u3066\u3001\u5074\u9396\uff08\u70ad\u7d20\uff1a\u9ec4\u8272\uff09\u306e\u914d\u5ea7\u751f\u6210\u3092\u884c\u3044\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"627\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31-1024x627.png\" alt=\"\" class=\"wp-image-2779\" style=\"width:406px;height:auto\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31-1024x627.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31-300x184.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31-768x470.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31-850x520.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f31.png 1086w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>RDKit\u306e&#8221;AllChem.ConstrainedEmbed&#8221;\u3092\u5229\u7528\u3059\u308b\u3053\u3068\u3067\u5b9f\u73fe\u3067\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<p><strong>core_embedded.py\uff1a<\/strong><\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>from rdkit.Chem import AllChem\nimport argparse\n\nparser = argparse.ArgumentParser(description=\"core_embedded.py\")\nparser.add_argument(\"input1\", help=\"mol of core structure\")\nparser.add_argument(\"input2\", help=\"smiles of molecules\")\nparser.add_argument(\"output\", help=\"sdf of molecules\")\n\ndef main():\n    args = parser.parse_args()\n    core_file = args.input1\n    smi_file = args.input2\n    out_file = args.output\n    \n    core = Chem.MolFromMolFile(core_file)\n    mols = &#091;Chem.AddHs(mol) for mol in Chem.SmilesMolSupplier(smi_file,delimiter='\\t',titleLine=0) if mol is not None]\n \n    fw = Chem.SDWriter(out_file)\n    for mol in mols:\n        try:\n            AllChem.ConstrainedEmbed(mol, core)\n            fw.write(mol)\n        except:\n            print(f\"{mol.GetProp('_Name')} doesn't have core structure\")\n    fw.close()\n\nif __name__ == '__main__':\n    main()<\/code><\/pre>\n\n\n\n<p>\u4e0a\u8a18\u306e\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u4f7f\u3063\u3066\u914d\u5ea7\u751f\u6210\u3092\u884c\u3063\u3066\u307f\u307e\u3059\u3002<br>$ python core_embedded.py core.sdf test_cpds.smi test_cpds.sdf<br><br>\u3000core.sdf\uff1a\u56fa\u5b9a\u3057\u305f\u3044\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7<br>\u3000test_cpds.smi\uff1a\u5206\u5b50\u306eSMILES(\u56fa\u5b9a\u3057\u305f\u3044\u9aa8\u683c\u3092\u90e8\u5206\u69cb\u9020\u3068\u3057\u3066\u542b\u3093\u3067\u3044\u308b\u3053\u3068)<br>\u3000test_cpds.sdf\uff1a\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u304c\u56fa\u5b9a\u3055\u308c\u305f\u5206\u5b50\u306e\u7acb\u4f53\u914d\u5ea7\uff08\u51fa\u529b\u30d5\u30a1\u30a4\u30eb\uff09<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"591\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32-1024x591.png\" alt=\"\" class=\"wp-image-2780\" style=\"width:486px;height:auto\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32-1024x591.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32-300x173.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32-768x444.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32-850x491.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f32.png 1148w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u751f\u6210\u3055\u308c\u305f\u7acb\u4f53\u914d\u5ea7\uff08\u70ad\u7d20\uff1a\u7dd1\uff09\u3092\u307f\u308b\u3068\u3001\u9aa8\u683c\u306f\u7d50\u6676\u69cb\u9020\u306e\u7acb\u4f53\u914d\u5ea7\uff08\u70ad\u7d20\uff1a\u7070\u8272\uff09\u3068\u540c\u3058\u3067\u3059\u304c\u3001\u5074\u9396\u306e\u7acb\u4f53\u914d\u5ea7\uff08\u70ad\u7d20\uff1a\u9ec4\u8272\uff09\u306f\u7570\u306a\u308b\u3053\u3068\u304c\u5206\u304b\u308b\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u30c9\u30c3\u30ad\u30f3\u30b0<\/h2>\n\n\n\n<p>\u524d\u9805\u3067\u751f\u6210\u3057\u305f\u5206\u5b50\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u7528\u3044\u3066<a href=\"https:\/\/github.com\/gnina\/gnina\">GNINA<\/a>\u3092\u4f7f\u3063\u3066\u30c9\u30ad\u30f3\u30b0\u3092\u884c\u3044\u305f\u3044\u3068\u601d\u3044\u307e\u3059\u3002<br>$ gnina -r 5OQW_receptor.pdb -l test_cpds.sdf -o docked_test_cpds.sdf &#8211;autobox_ligand 5OQW_ligand.sdf &#8211;num_modes 1<br><br> 5OQW_receptor.pdb\uff1aXIAP\u306e\u69cb\u9020<br> test_cpds.sdf\uff1a\u524d\u9805\u3067\u751f\u6210\u3057\u305f\u5206\u5b50\u306e\u7acb\u4f53\u914d\u5ea7<br> docked_test_cpds.sdf\uff1a\u30c9\u30c3\u30ad\u30f3\u30b0\u306b\u3088\u308a\u5f97\u3089\u308c\u305f\u5206\u5b50\u306e\u7d50\u5408\u914d\u5ea7<br> 5OQW_ligand.sdf\uff1a\u7d50\u6676\u69cb\u9020\u306b\u542b\u307e\u308c\u3066\u3044\u308b\u963b\u5bb3\u5264\u306e\u7acb\u4f53\u914d\u5ea7<\/p>\n\n\n\n<figure class=\"wp-block-image size-large is-resized\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"594\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33-1024x594.png\" alt=\"\" class=\"wp-image-2781\" style=\"width:509px;height:auto\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33-1024x594.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33-300x174.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33-768x445.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33-850x493.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/09\/\u56f33.png 1159w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u30c9\u30c3\u30ad\u30f3\u30b0\u306b\u3088\u308b\u4e88\u6e2c\u914d\u5ea7\uff08\u70ad\u7d20\uff1a\u7dd1\uff09\u3092\u307f\u308b\u3068\u7d50\u6676\u69cb\u9020\uff08\u70ad\u7d20\uff1a\u7070\u8272 or \u9ec4\u8272\uff09\u3068\u3088\u304f\u91cd\u306a\u3063\u3066\u3044\u308b\u3068\u601d\u3044\u307e\u3059\u3002\u4eca\u56de\u306e\u624b\u9806\u3092\u7528\u3044\u3066\u3001\u5074\u9396\u69cb\u9020\u306e\u7570\u306a\u308b\u5206\u5b50\u3092\u8907\u6570\u767a\u751f\u3055\u305b\u3001\u30c9\u30c3\u30ad\u30f3\u30b0\u3092\u884c\u3046\u3053\u3068\u3067\u3001\u5074\u9396\u69cb\u9020\u306e\u6700\u9069\u5316\u306a\u3069\u306b\u5229\u7528\u3067\u304d\u308b\u3068\u601d\u3044\u307e\u3059\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u5409\u68ee\u3067\u3059\u3002\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u591a\u304f\u306f\u3001\u74b0\u69cb\u9020\u306b\u304a\u3051\u308b\u30a4\u30b9\u5f62\u3068\u821f\u5f62\u306a\u3069\u306e\u5909\u5316\u3092\u8003\u616e\u3067\u304d\u306a\u3044\u305f\u3081\u3001\u521d\u671f\u914d\u5ea7\u304c\u30c9\u30c3\u30ad\u30f3\u30b0\u306e\u7d50\u679c\u306b\u4e0e\u3048\u308b\u5f71\u97ff\u304c\u5927\u304d\u3044\u3068\u601d\u3044\u307e\u3059\u3002\u4eca\u56de\u306f\u3001\u307e\u305a\u306f\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u3092\u56fa&#8230;<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[118,8],"tags":[],"class_list":["post-2778","post","type-post","status-publish","format-standard","hentry","category-ai-drug-discovery","category-docking"],"yoast_head":"<!-- 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content=\"2025-09-25T08:51:26+00:00\" \/>\n<meta name=\"author\" content=\"\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240 \u5409\u68ee \u7be4\u53f2\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"\u57f7\u7b46\u8005\" \/>\n\t<meta name=\"twitter:data1\" content=\"\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240 \u5409\u68ee \u7be4\u53f2\" \/>\n\t<meta name=\"twitter:label2\" content=\"\u63a8\u5b9a\u8aad\u307f\u53d6\u308a\u6642\u9593\" \/>\n\t<meta name=\"twitter:data2\" content=\"5\u5206\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.insilico.jp\/blog\/2025\/09\/16\/core_embed_docking\/\",\"url\":\"https:\/\/www.insilico.jp\/blog\/2025\/09\/16\/core_embed_docking\/\",\"name\":\"\u9aa8\u683c\u306e\u7acb\u4f53\u914d\u5ea7\u306e\u56fa\u5b9a\u3068\u30c9\u30c3\u30ad\u30f3\u30b0 - In Silico 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