{"id":2648,"date":"2025-05-19T17:19:07","date_gmt":"2025-05-19T08:19:07","guid":{"rendered":"https:\/\/www.insilico.jp\/blog\/?p=2648"},"modified":"2025-06-19T15:25:32","modified_gmt":"2025-06-19T06:25:32","slug":"gnina_docking","status":"publish","type":"post","link":"https:\/\/www.insilico.jp\/blog\/2025\/05\/19\/gnina_docking\/","title":{"rendered":"GNINA\u3092\u7528\u3044\u305f\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3"},"content":{"rendered":"\n<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002<br>\u4eca\u56de\u306f\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u7528\u3044\u3066\u3001\u4f4e\u5206\u5b50\u5316\u5408\u7269\u3068\u6a19\u7684\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u3092\u884c\u3063\u3066\u3044\u304d\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u53c2\u8003\u8ad6\u6587<br>GNINA 1.0: molecular docking with deep learning<br>(Andrew T. McNutt, Paul Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, David Ryan Koes, <em>Journal of Cheminformatics<\/em> <strong>2021<\/strong>, <em>13<\/em>, 43)<br><a href=\"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-021-00522-2\">https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-021-00522-2<\/a><br>GNINA 1.3: the next increment in molecular docking with deep learning<br>(Andrew T. McNutt, Yanjing Li, Rocco Meli, Rishal Aggarwal, David Ryan Koes, <em>Journal of Cheminformatics<\/em>, <strong>2025<\/strong>, <em>17<\/em>, 28.)<br><a href=\"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-025-00973-x\">https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-025-00973-x<\/a><\/p>\n\n\n\n<p>\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306f\u5546\u7528\u30fb\u975e\u5546\u7528\u554f\u308f\u305a\u69d8\u3005\u306a\u7a2e\u985e\u306e\u3082\u306e\u304c\u958b\u767a\u3055\u308c\u3066\u3044\u307e\u3059\u304c\u3001\u4eca\u56de\u7d39\u4ecb\u3059\u308bGNINA\uff08Generative Neural Network for Interactive Applications\uff09\u306f\u3001\u65e2\u5b58\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3067\u3042\u308bAutodock Vina\u3084Smina\u306b\u30c7\u30a3\u30fc\u30d7\u30e9\u30fc\u30cb\u30f3\u30b0\u3092\u7d71\u5408\u3057\u30013D-\u7573\u307f\u8fbc\u307f\u30cb\u30e5\u30fc\u30e9\u30eb\u30cd\u30c3\u30c8\u30ef\u30fc\u30af\uff083D-CNN\uff09\u3092\u7528\u3044\u3066\u3001\u3088\u308a\u67d4\u8edf\u3067\u9ad8\u7cbe\u5ea6\u306a\u30b9\u30b3\u30a2\u30ea\u30f3\u30b0\u3092\u53ef\u80fd\u306b\u3057\u305f\u3082\u306e\u306b\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<p>\u52d5\u4f5c\u74b0\u5883<br>Intel Core i9-10900K<br>Nvidia GeForce RTX 3070<br>Windows 11 home<br>WSL 2.4.13.0<br>Ubuntu 24.04<br>conda 25.3.1<\/p>\n\n\n\n<p>\u30ed\u30fc\u30ab\u30eb\u74b0\u5883\u3067\u5229\u7528\u3059\u308b\u5834\u5408\u306fCUDA&gt;12.0\u304c\u8981\u6c42\u3055\u308c\u3066\u3044\u307e\u3059\u306e\u3067\u3001Maxwell\u4e16\u4ee3\u4ee5\u964d\u306eGPU\uff08GTX 750\u4ee5\u964d\uff09\u304c\u5fc5\u8981\u3068\u306a\u308a\u307e\u3059\u3002GPU\u74b0\u5883\u304c\u306a\u3044\u5834\u5408\u306fGoogle Colab\u3067\u5b9f\u88c5\u3055\u308c\u3066\u3044\u307e\u3059\u306e\u3067\u3001\u5f8c\u307b\u3069\u4f7f\u7528\u6cd5\u3092\u89e3\u8aac\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">GNINA\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h2>\n\n\n\n<p>GNINA\u306fLinux\u74b0\u5883\u3067\u306e\u52d5\u4f5c\u304c\u30b5\u30dd\u30fc\u30c8\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u4eca\u56de\u306fWindows\u3067\u306eLinux\u4eee\u60f3\u74b0\u5883\u3078\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3092\u7d39\u4ecb\u3057\u307e\u3059\u3002\u307e\u305a\u306f\u4eee\u60f3\u74b0\u5883\u3092\u4f5c\u6210\u3057\u3001CUDA\u3068\u95a2\u9023\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002<br>WSL\u306e\u5834\u5408\u306f<a href=\"https:\/\/docs.nvidia.com\/cuda\/wsl-user-guide\/contents.html\">https:\/\/docs.nvidia.com\/cuda\/wsl-user-guide\/contents.html<\/a>\u306e\u30ac\u30a4\u30c9\u306b\u3057\u305f\u304c\u3063\u3066\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u307e\u3059\u3002<br>Linux\u306e\u5834\u5408\u306f<a href=\"https:\/\/developer.nvidia.com\/cuda-downloads\">https:\/\/developer.nvidia.com\/cuda-downloads<\/a>\u304b\u3089deb (network) \u3092\u9078\u629e\u3057\u3066\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u7528\u30b3\u30de\u30f3\u30c9\u3092\u53d6\u5f97\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda create -n GNINA python=3.12\n$ conda activate GNINA\n$ sudo apt-key del 7fa2af80\n$ wget https:\/\/developer.download.nvidia.com\/compute\/cuda\/repos\/wsl-ubuntu\/x86_64\/cuda-wsl-ubuntu.pin\n$ sudo mv cuda-wsl-ubuntu.pin \/etc\/apt\/preferences.d\/cuda-repository-pin-600\n$ wget https:\/\/developer.download.nvidia.com\/compute\/cuda\/12.8.1\/local_installers\/cuda-repo-wsl-ubuntu-12-8-local_12.8.1-1_amd64.deb\n$ sudo dpkg -i cuda-repo-wsl-ubuntu-12-8-local_12.8.1-1_amd64.deb\n$ sudo cp \/var\/cuda-repo-wsl-ubuntu-12-8-local\/cuda-*-keyring.gpg \/usr\/share\/keyrings\/\n$ sudo apt-get update\n$ sudo apt-get -y install cuda-toolkit-12-8\n\n$ wget https:\/\/developer.download.nvidia.com\/compute\/cudnn\/9.8.0\/local_installers\/cudnn-local-repo-ubuntu2404-9.8.0_1.0-1_amd64.deb\n$ sudo dpkg -i cudnn-local-repo-ubuntu2404-9.8.0_1.0-1_amd64.deb\n$ sudo cp \/var\/cudnn-local-repo-ubuntu2404-9.8.0\/cudnn-*-keyring.gpg \/usr\/share\/keyrings\/\n$ sudo apt-get update\n$ sudo apt-get -y install cudnn-cuda-12\n\n$ echo 'export PATH=\/usr\/local\/cuda-12.8\/bin${PATH:+:${PATH}}' &gt;&gt; ~\/.bashrc\n$ echo 'export LD_LIBRARY_PATH=\/usr\/local\/cuda-12.8\/lib64:${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}'  &gt;&gt; ~\/.bashrc\n$ source ~\/.bashrc<\/code><\/pre>\n\n\n\n<p>\u7d9a\u3044\u3066OpenBabel\u3068\u5fc5\u8981\u306a\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3092\u3057\u3066\u3044\u304d\u307e\u3059\u3002\u4eca\u56de\u306fPython\u95a2\u9023\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306fConda\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda activate GNINA\n$ conda install -c conda-forge numpy=1.26 pytest -y\n$ apt-get install build-essential git cmake wget swig libboost-all-dev libeigen3-dev libgoogle-glog-dev libprotobuf-dev protobuf-compiler libhdf5-dev libatlas-base-dev  librdkit-dev libjsoncpp-dev\n\n$ git clone https:\/\/github.com\/openbabel\/openbabel.git\n$ cd openbabel\n$ mkdir build\n$ cd build\n$ cmake -DWITH_MAEPARSER=OFF -DWITH_COORDGEN=OFF -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON ..\n$ make -j8\n$ sudo make install\n$ source ~\/.bashrc<\/code><\/pre>\n\n\n\n<p>\u6700\u5f8c\u306bGNINA\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3092\u3057\u3066\u3044\u304d\u307e\u3059\u3002cmake\u304ccuDNN\u306ePATH\u3092\u53c2\u7167\u3067\u304d\u306a\u304b\u3063\u305f\u306e\u3067PATH\u3092\u660e\u793a\u3057\u3066\u3044\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ conda activate GNINA\n$ cd ~\n$ git clone https:\/\/github.com\/gnina\/gnina.git\n$ cd gnina\n$ mkdir build\n$ cd build\n$ cmake -DCUDNN_INCLUDE_PATH=\/usr\/include -DCUDNN_LIBRARY_PATH=\/usr\/lib\/x86_64-linux-gnu\/libcudnn.so ..\n$ make -j8\n$ sudo make install<\/code><\/pre>\n\n\n\n<p>gnina\u3068\u5165\u529b\u3057\u3066\u4ee5\u4e0b\u306e\u753b\u9762\u304c\u8868\u793a\u3055\u308c\u308c\u3070\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u5b8c\u4e86\u3067\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ gnina\n              _\n             (_)\n   __ _ _ __  _ _ __   __ _\n  \/ _` | '_ \\| | '_ \\ \/ _` |\n | (_| | | | | | | | | (_| |\n  \\__, |_| |_|_|_| |_|\\__,_|\n   __\/ |\n  |___\/\n\ngnina  master:25e64da   Built Apr 28 2025.\ngnina is based on smina and AutoDock Vina.\nPlease cite appropriately.<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u5b9f\u884c<\/h2>\n\n\n\n<p>\u30c1\u30e5\u30fc\u30c8\u30ea\u30a2\u30eb\u306b\u8a18\u8f09\u3055\u308c\u3066\u3044\u308bMAPK\u306e\u963b\u5bb3\u5264\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<br>PDB\u304b\u3089\u69cb\u9020\u60c5\u5831\u3092\u53d6\u5f97\u3057\u3001\u30ec\u30bb\u30d7\u30bf\u30fc\u3068\u30ea\u30ac\u30f3\u30c9\u3092\u305d\u308c\u305e\u308c\u4fdd\u5b58\u3057\u3001GNINA\u3092\u4f7f\u7528\u3057\u3066\u30c9\u30c3\u30ad\u30f3\u30b0\u3057\u307e\u3059\u3002\u30b3\u30de\u30f3\u30c9\u306f\u305d\u308c\u305e\u308c -r \u304c\u30ec\u30bb\u30d7\u30bf\u30fc\u306e\u6307\u5b9a\u3001-l \u304c\u30ea\u30ac\u30f3\u30c9\u306e\u6307\u5b9a\u3001&#8211;autobox_ligand \u306f\u30c9\u30c3\u30ad\u30f3\u30b0\u7bc4\u56f2\u306e\u6307\u5b9a\u3067\u4eca\u56de\u306f\u3059\u3067\u306b\u30ea\u30ac\u30f3\u30c9\u5206\u5b50\u304c\u5165\u3063\u3066\u3044\u308b\u9818\u57df\u3092\u6307\u5b9a\u3057\u3066\u3044\u307e\u3059\u3001-o \u306f\u30a2\u30a6\u30c8\u30d7\u30c3\u30c8\u30d5\u30a1\u30a4\u30eb\u306e\u6307\u5b9a\u3001&#8211;seed \u306f\u30b7\u30fc\u30c9\u5024\u306e\u6307\u5b9a\u3067\u5165\u529b\u3057\u306a\u3044\u5834\u5408\u30e9\u30f3\u30c0\u30e0\u30b7\u30fc\u30c9\u3068\u306a\u308a\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ wget http:\/\/files.rcsb.org\/download\/3ERK.pdb\n$ grep ATOM 3ERK.pdb &gt; rec.pdb\n$ grep SB4 3ERK.pdb &gt; lig.pdb\n$ gnina -r rec.pdb -l lig.pdb --autobox_ligand lig.pdb -o docked.sdf --seed 0\n              _\n             (_)\n   __ _ _ __  _ _ __   __ _\n  \/ _` | '_ \\| | '_ \\ \/ _` |\n | (_| | | | | | | | | (_| |\n  \\__, |_| |_|_|_| |_|\\__,_|\n   __\/ |\n  |___\/\n\ngnina  master:25e64da   Built Apr 28 2025.\ngnina is based on smina and AutoDock Vina.\nPlease cite appropriately.\n\nCommandline: gnina -r rec.pdb -l lig.pdb --autobox_ligand lig.pdb -o docked.sdf --seed 0\n==============================\n*** Open Babel Warning  in PerceiveBondOrders\n  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders\n\nUsing random seed: 0\n\n0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\n\nmode |  affinity  |  intramol  |    CNN     |   CNN\n     | (kcal\/mol) | (kcal\/mol) | pose score | affinity\n-----+------------+------------+------------+----------\n    1       -8.50       -0.79       0.9777      7.179\n    2       -8.51       -0.84       0.9650      7.199\n    3       -8.30       -0.72       0.4390      6.297\n    4       -7.68       -0.65       0.3015      5.951\n    5       -6.12       -0.53       0.2668      6.026\n    6       -7.59       -0.65       0.2356      5.685\n    7       -6.92       -0.47       0.2143      5.956\n    8       -6.36       -0.95       0.2086      5.438\n    9       -6.90       -0.77       0.1767      4.250<\/code><\/pre>\n\n\n\n<p>\u8a08\u7b97\u304c\u5b9f\u884c\u3055\u308c\u308b\u3068\u751f\u6210\u3055\u308c\u305f\u30b3\u30f3\u30d5\u30a9\u30e1\u30fc\u30b7\u30e7\u30f3\u306e\u30a2\u30d5\u30a3\u30cb\u30c6\u30a3\u30fc\u3068\u30b9\u30b3\u30a2\u304c\u8868\u793a\u3055\u308c\u3001\u7d50\u679c\u306fdocked.sdf\u306b\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u51fa\u529b\u3055\u308c\u305f\u69cb\u9020\u3092PyMOL\u3092\u4f7f\u3063\u3066\u8868\u793a\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"532\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-1024x532.png\" alt=\"\" class=\"wp-image-2668\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-1024x532.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-300x156.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-768x399.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-1536x798.png 1536w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk-850x442.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk.png 1816w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u69cb\u9020\uff08PDB:1ERK\uff09, \u30d4\u30f3\u30af\uff1a\u7d50\u6676\u69cb\u9020\u4e2d\u306e\u30ea\u30ac\u30f3\u30c9, \u9752\uff1a\u30c9\u30c3\u30ad\u30f3\u30b0\u3055\u308c\u305f\u30ea\u30ac\u30f3\u30c9<\/p>\n\n\n\n<p>\u7d50\u6676\u69cb\u9020\u3068\u975e\u5e38\u306b\u8fd1\u3044\u5f62\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u7d50\u679c\u304c\u5f97\u3089\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u30b3\u30d0\u30ec\u30f3\u30c8\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u5b9f\u884c<\/h2>\n\n\n\n<p>GNINA1.3\u306b\u306f\u5171\u6709\u7d50\u5408\u6027\u963b\u5bb3\u5264\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u6a5f\u80fd\u304c\u5b9f\u88c5\u3055\u308c\u3066\u3044\u307e\u3059\u3002\u4f8b\u3068\u3057\u3066\u30da\u30cb\u30b7\u30ea\u30f3\u7d50\u5408\u30bf\u30f3\u30d1\u30af\u8cea\u3068\u30bb\u30d5\u30ed\u30ad\u30b7\u30e0\u306e\u30b3\u30d0\u30ec\u30f3\u30c8\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002\u540c\u69d8\u306bPDB\u304b\u3089\u69cb\u9020\u60c5\u5831\u3092\u53d6\u5f97\u3057\u3001\u30ec\u30bb\u30d7\u30bf\u30fc\u3068\u30ea\u30ac\u30f3\u30c9\u3092\u305d\u308c\u305e\u308c\u4fdd\u5b58\u3057\u3001GNINA\u3092\u4f7f\u7528\u3057\u3066\u30c9\u30c3\u30ad\u30f3\u30b0\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ wget http:\/\/files.rcsb.org\/download\/1QMF.pdb<\/code><\/pre>\n\n\n\n<p>\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u305fPDB\u30d5\u30a1\u30a4\u30eb\u3092PyMOL\u3067\u958b\u304d\u3001\u6c34\u5206\u5b50\u3068\u30ea\u30ac\u30f3\u30c9\u5206\u5b50\u3092\u524a\u9664\u3057\u305f\u3082\u306e\u3092\u30ec\u30bb\u30d7\u30bf\u30fc\u3068\u3057\u3066\u3001\u30bb\u30d5\u30ed\u30ad\u30b7\u30e0\u306e\u307f\u3092\u30ea\u30ac\u30f3\u30c9\u3068\u3057\u3066\u305d\u308c\u305e\u308c\u4fdd\u5b58\u3057\u307e\u3059\u3002\u30b3\u30d0\u30ec\u30f3\u30c8\u30c9\u30c3\u30ad\u30f3\u30b0\u306e\u5834\u5408\u306f\u5171\u6709\u7d50\u5408\u3092\u5f62\u6210\u3059\u308b\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\u3068\u30ea\u30ac\u30f3\u30c9\u306e\u539f\u5b50\u3092\u305d\u308c\u305e\u308c\u6307\u5b9a\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002&#8211;covalent_rec_atom \u304c\u30ec\u30bb\u30d7\u30bf\u30fc\u306e\u30a2\u30df\u30ce\u9178\u6b8b\u57fa\u306e\u6307\u5b9a\u3067\u30c1\u30a7\u30a4\u30f3\uff1a\u6b8b\u57fa\u756a\u53f7\uff1a\u539f\u5b50\u306e\u5f62\u3067\u5165\u529b\u3057\u3001\u539f\u5b50\u306f\u8a72\u5f53\u3059\u308b\u5834\u6240\u3092PyMOL\u3067\u9078\u629e\u3059\u308b\u3068\u8868\u793a\u3055\u308c\u307e\u3059\u3002&#8211;covalent_lig_atom_pattern \u304c\u30ea\u30ac\u30f3\u30c9\u306e\u7d50\u5408\u539f\u5b50\u3067SMART\u5f62\u5f0f\u3067\u6307\u5b9a\u3057\u307e\u3059\u3002<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>$ gnina -r rec.pdb -l lig.pdb --autobox_ligand lig.pdb --covalent_rec_atom A:337:OG --covalent_lig_atom_pattern 'CCCSCCCN' -o docked.sdf --seed 0\n              _\n             (_)\n   __ _ _ __  _ _ __   __ _\n  \/ _` | '_ \\| | '_ \\ \/ _` |\n | (_| | | | | | | | | (_| |\n  \\__, |_| |_|_|_| |_|\\__,_|\n   __\/ |\n  |___\/\n\ngnina  master:25e64da   Built Apr 28 2025.\ngnina is based on smina and AutoDock Vina.\nPlease cite appropriately.\n\nWARNING: CNN scoring not yet calibrated for covalent docking.  Recommend running with --cnn_scoring none\nCommandline: gnina -r rec.pdb -l lig.pdb --autobox_ligand lig.pdb --covalent_rec_atom A:337:OG --covalent_lig_atom_pattern CCCSCCCN -o docked.sdf --seed 0\n==============================\n*** Open Babel Warning  in PerceiveBondOrders\n  Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders\n\nUsing random seed: 0\n\n0%   10   20   30   40   50   60   70   80   90   100%\n|----|----|----|----|----|----|----|----|----|----|\n***************************************************\n\nmode |  affinity  |  intramol  |    CNN     |   CNN\n     | (kcal\/mol) | (kcal\/mol) | pose score | affinity\n-----+------------+------------+------------+----------\n    1       -8.78        0.00       0.6755      5.042\n    2       -8.66        0.00       0.6717      4.659\n    3       -7.69        0.00       0.6614      4.986\n    4       -8.97        0.00       0.6596      4.783\n    5       -8.17        0.00       0.6076      5.013\n    6       -5.13        0.00       0.5839      5.508\n    7       -6.74        0.00       0.5415      5.280\n    8       -8.89        0.00       0.5245      4.588\n    9       -8.78        0.00       0.4824      4.571<\/code><\/pre>\n\n\n\n<p>\u540c\u69d8\u306b\u51fa\u529b\u3055\u308c\u305f\u69cb\u9020\u3092PyMOL\u3092\u4f7f\u3063\u3066\u8868\u793a\u3057\u3066\u307f\u307e\u3057\u3087\u3046\u3002<\/p>\n\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"532\" src=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-1024x532.png\" alt=\"\" class=\"wp-image-2670\" srcset=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-1024x532.png 1024w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-300x156.png 300w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-768x399.png 768w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-1536x798.png 1536w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf-850x442.png 850w, https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/1qmf.png 1816w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n\n\n\n<p>\u30bf\u30f3\u30d1\u30af\u8cea\u69cb\u9020\uff08PDB:1QMF\uff09, \u30d4\u30f3\u30af\uff1a\u7d50\u6676\u69cb\u9020\u4e2d\u306e\u30ea\u30ac\u30f3\u30c9, \u9752\uff1a\u30c9\u30c3\u30ad\u30f3\u30b0\u3055\u308c\u305f\u30ea\u30ac\u30f3\u30c9<\/p>\n\n\n\n<p>\u3053\u3061\u3089\u3082\u7d50\u6676\u69cb\u9020\u3068\u975e\u5e38\u306b\u8fd1\u3044\u5f62\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u7d50\u679c\u304c\u5f97\u3089\u308c\u307e\u3057\u305f\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Google Colab\u3067\u306e\u4f7f\u7528<\/h2>\n\n\n\n<p>Colab\u306e\u30da\u30fc\u30b8<a href=\"https:\/\/colab.research.google.com\/drive\/1QYo5QLUE80N_G28PlpYs6OKGddhhd931?usp=sharing\">https:\/\/colab.research.google.com\/drive\/1QYo5QLUE80N_G28PlpYs6OKGddhhd931?usp=sharing<\/a>\u306b\u30a2\u30af\u30bb\u30b9\u3057\u307e\u3059\u3002<br>\u53f3\u4e0a\u306e\u305d\u306e\u4ed6\u306e\u63a5\u7d9a\u30aa\u30d7\u30b7\u30e7\u30f3\u304b\u3089\u30e9\u30f3\u30bf\u30a4\u30e0\u306e\u30bf\u30a4\u30d7\u306e\u5909\u66f4\u3092\u9078\u629e\u3057\u3001\u30e9\u30f3\u30bf\u30a4\u30e0\u306e\u30bf\u30a4\u30d7\u306fPython 3\u3092\u30cf\u30fc\u30c9\u30a6\u30a7\u30a2 \u30a2\u30af\u30bb\u30e9\u30ec\u30fc\u30bf\u306fGPU\u3092\u9078\u629e\u3057\u307e\u3059\u3002\u30e9\u30f3\u30bf\u30a4\u30e0\u304b\u3089\u5168\u3066\u306e\u30bb\u30eb\u3092\u5b9f\u884c\u3092\u9078\u629e\u3059\u308b\u3068\u9806\u6b21\u5b9f\u884c\u3055\u308c\u3001\u524d\u8ff0\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3068\u540c\u4e00\u306e\u7d50\u679c\u304c\u51fa\u529b\u3055\u308c\u307e\u3059\u3002\u4efb\u610f\u306e\u30bf\u30f3\u30d1\u30af\u8cea\u3067\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u3092\u5b9f\u884c\u3059\u308b\u5834\u5408\u306f\u3001PDB\u304b\u3089\u53d6\u5f97\u3059\u308b\u30bf\u30f3\u30d1\u30af\u8cea\u3092\u5909\u66f4\u3059\u308b\u304b\u3001\u7528\u610f\u3057\u305f\u69cb\u9020\u60c5\u5831\u3092Google drive\u306b\u30a2\u30c3\u30d7\u30ed\u30fc\u30c9\u3057\u3066\u5b9f\u884c\u3057\u3066\u307f\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u304a\u308f\u308a\u306b<\/h2>\n\n\n\n<p>\u3053\u308c\u307e\u3067\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u306f\u8907\u96d1\u306a\u5165\u529b\u304c\u5fc5\u8981\u3067\u3057\u305f\u304c\u3001\u4eca\u56de\u7d39\u4ecb\u3057\u305fGNINA\u306f\u30b7\u30f3\u30d7\u30eb\u306a\u5165\u529b\u5f62\u5f0f\u306b\u5bfe\u5fdc\u3057\u3066\u304a\u308a\u3001\u8a08\u7b97\u3082\u975e\u5e38\u306b\u9ad8\u901f\u3067\u3059\u3002AlphaFold\u306a\u3069\u3067\u4e88\u6e2c\u3055\u308c\u305f\u69cb\u9020\u3082\u5165\u529b\u306b\u4f7f\u7528\u3059\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u306e\u3067\u3001\u5275\u85ac\u7814\u7a76\u306b\u304a\u5f79\u7acb\u3066\u304f\u3060\u3055\u3044\u3002<\/p>\n\n\n\n<p>\u524d\u56de\u8a18\u4e8b<br>BR-SAScore\u306b\u3088\u308b\u5206\u5b50\u306e\u5408\u6210\u96e3\u6613\u5ea6\u4e88\u6e2c<br><a href=\"https:\/\/www.insilico.jp\/blog\/2025\/04\/24\/br_sascore\/\">https:\/\/www.insilico.jp\/blog\/2025\/04\/24\/br_sascore\/<\/a><br>\u6b21\u56de\u8a18\u4e8b<br>AiZynthFinder\u306b\u3088\u308b\u9006\u5408\u6210\u89e3\u6790<br><a href=\"https:\/\/www.insilico.jp\/blog\/2025\/06\/05\/aizynthfinder_retrosynthesis\/\">https:\/\/www.insilico.jp\/blog\/2025\/06\/05\/aizynthfinder_retrosynthesis\/<\/a><\/p>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002\u4eca\u56de\u306f\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u7528\u3044\u3066\u3001\u4f4e\u5206\u5b50\u5316\u5408\u7269\u3068\u6a19\u7684\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u3092\u884c\u3063\u3066\u3044\u304d\u307e\u3059\u3002 \u53c2\u8003\u8ad6\u6587GNINA 1.0: molecular docki&#8230;<\/p>\n","protected":false},"author":7,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[118,8],"tags":[],"class_list":["post-2648","post","type-post","status-publish","format-standard","hentry","category-ai-drug-discovery","category-docking"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.3.1 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>GNINA\u3092\u7528\u3044\u305f\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3 - In Silico \u5275\u85ac<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.insilico.jp\/blog\/2025\/05\/19\/gnina_docking\/\" \/>\n<meta property=\"og:locale\" content=\"ja_JP\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"GNINA\u3092\u7528\u3044\u305f\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3 - In Silico \u5275\u85ac\" \/>\n<meta property=\"og:description\" content=\"\u7406\u8ad6\u5275\u85ac\u7814\u7a76\u6240\u306e\u91d1\u5b50\u4fe1\u4eba\u3067\u3059\u3002\u4eca\u56de\u306f\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3092\u7528\u3044\u3066\u3001\u4f4e\u5206\u5b50\u5316\u5408\u7269\u3068\u6a19\u7684\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u3092\u884c\u3063\u3066\u3044\u304d\u307e\u3059\u3002 \u53c2\u8003\u8ad6\u6587GNINA 1.0: molecular docki...\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.insilico.jp\/blog\/2025\/05\/19\/gnina_docking\/\" \/>\n<meta property=\"og:site_name\" content=\"In Silico \u5275\u85ac\" \/>\n<meta property=\"article:published_time\" content=\"2025-05-19T08:19:07+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-06-19T06:25:32+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.insilico.jp\/blog\/wp-content\/uploads\/2025\/05\/3erk.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1816\" \/>\n\t<meta property=\"og:image:height\" content=\"944\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"author\" content=\"kaneko\" \/>\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=\"kaneko\" \/>\n\t<meta name=\"twitter:label2\" content=\"\u63a8\u5b9a\u8aad\u307f\u53d6\u308a\u6642\u9593\" \/>\n\t<meta name=\"twitter:data2\" content=\"19\u5206\" \/>\n<script type=\"application\/ld+json\" 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