{
  "id": 503096,
  "title": "[placeholder] experiments results with AutoDock Vina",
  "url": "/competitions/leash-BELKA/discussion/503096",
  "author_name": "",
  "post_date": "2024-05-16T04:15:41.856927200Z",
  "votes": 8,
  "comment_count": 3,
  "views": 0,
  "content": "<p><strong>WARNING !!!!</strong><br>\nI am not a chemist. I am reading information from the wen and figuring what to do.<br>\nIf i make any wrong steps please advise. Thanks! </p>\n<h1>[step.1: install software]  completed</h1>\n<ul>\n<li>i choose the simplest : DOCKSTRING</li>\n<li><a href=\"https://github.com/dockstring/dockstring\" target=\"_blank\">https://github.com/dockstring/dockstring</a></li>\n<li><a href=\"https://dockstring.github.io/\" target=\"_blank\">https://dockstring.github.io/</a></li>\n<li>just need to install rdkit,openbabel,pymol</li>\n<li>then \"python3 -m pip install dockstring\"</li>\n<li>run the demo<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F10f327574b3e51ba442eed8503aec313%2FSelection_124.png?generation=1715832750604319&amp;alt=media\"><br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2Fb412d2afeef25ebc42b94fbe7969a443%2FSelection_125.png?generation=1715832764139261&amp;alt=media\"></li>\n</ul>\n<p>score printed is \"-11.9\". This is the value i need for my experiments later.</p>\n<h1>[step.2: prepare input files of kaggle dataset]  in progress</h1>\n<p>i need these file for the target protein</p>\n<pre><code>    &lt;name&gt;.pdbqt    protein structure including partial charges.\n    &lt;name&gt;.txt   coordinates   search box.\n</code></pre>\n<p>if you have good suggestion on how to generate these, let me know.</p>",
  "messages": [
    {
      "id": "2815754",
      "postDate": "05/16/2024 04:15:41",
      "content": "<p><strong>WARNING !!!!</strong><br>\nI am not a chemist. I am reading information from the wen and figuring what to do.<br>\nIf i make any wrong steps please advise. Thanks! </p>\n<h1>[step.1: install software]  completed</h1>\n<ul>\n<li>i choose the simplest : DOCKSTRING</li>\n<li><a href=\"https://github.com/dockstring/dockstring\" target=\"_blank\">https://github.com/dockstring/dockstring</a></li>\n<li><a href=\"https://dockstring.github.io/\" target=\"_blank\">https://dockstring.github.io/</a></li>\n<li>just need to install rdkit,openbabel,pymol</li>\n<li>then \"python3 -m pip install dockstring\"</li>\n<li>run the demo<br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F10f327574b3e51ba442eed8503aec313%2FSelection_124.png?generation=1715832750604319&amp;alt=media\"><br>\n<img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2Fb412d2afeef25ebc42b94fbe7969a443%2FSelection_125.png?generation=1715832764139261&amp;alt=media\"></li>\n</ul>\n<p>score printed is \"-11.9\". This is the value i need for my experiments later.</p>\n<h1>[step.2: prepare input files of kaggle dataset]  in progress</h1>\n<p>i need these file for the target protein</p>\n<pre><code>    &lt;name&gt;.pdbqt    protein structure including partial charges.\n    &lt;name&gt;.txt   coordinates   search box.\n</code></pre>\n<p>if you have good suggestion on how to generate these, let me know.</p>",
      "rawMarkdown": "**WARNING !!!!**\nI am not a chemist. I am reading information from the wen and figuring what to do.\nIf i make any wrong steps please advise. Thanks! \n\n# [step.1: install software]  completed\n- i choose the simplest : DOCKSTRING\n- https://github.com/dockstring/dockstring\n- https://dockstring.github.io/\n- just need to install rdkit,openbabel,pymol\n- then \"python3 -m pip install dockstring\"\n- run the demo\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F10f327574b3e51ba442eed8503aec313%2FSelection_124.png?generation=1715832750604319&alt=media)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2Fb412d2afeef25ebc42b94fbe7969a443%2FSelection_125.png?generation=1715832764139261&alt=media)\n\nscore printed is \"-11.9\". This is the value i need for my experiments later.\n\n# [step.2: prepare input files of kaggle dataset]  in progress\ni need these file for the target protein\n```\n    <name>_target.pdbqt contains the the protein structure including partial charges.\n    <name>_conf.txt contains the coordinates of the search box.\n```\n\nif you have good suggestion on how to generate these, let me know.",
      "votes": null
    },
    {
      "id": "2815759",
      "postDate": "05/16/2024 04:26:44",
      "content": "<p>related:<br>\nEasyDock : Python module to automate molecular docking</p>\n<ul>\n<li><a href=\"https://github.com/ci-lab-cz/easydock\" target=\"_blank\">https://github.com/ci-lab-cz/easydock</a></li>\n<li><a href=\"https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf\" target=\"_blank\">https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf</a></li>\n</ul>",
      "rawMarkdown": "related:\nEasyDock : Python module to automate molecular docking\n- https://github.com/ci-lab-cz/easydock\n- https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf",
      "votes": null
    },
    {
      "id": "2836502",
      "postDate": "05/26/2024 01:03:13",
      "content": "<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F5840699370202e9e194273bbee7f9bd5%2FSelection_146.png?generation=1716685386279962&amp;alt=media\"></p>\n<p>this is useful.<br>\ni find many tutorial on docking at youtube</p>",
      "rawMarkdown": "![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F5840699370202e9e194273bbee7f9bd5%2FSelection_146.png?generation=1716685386279962&alt=media)\n\nthis is useful.\ni find many tutorial on docking at youtube",
      "votes": null
    },
    {
      "id": "2844141",
      "postDate": "05/30/2024 01:14:50",
      "content": "<p>grid search for AutoDock Vina:<br>\n<a href=\"https://github.com/vukoviclab/docking-scan\" target=\"_blank\">https://github.com/vukoviclab/docking-scan</a></p>",
      "rawMarkdown": "grid search for AutoDock Vina:\nhttps://github.com/vukoviclab/docking-scan",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2815759,
      "author_name": "hengck23",
      "author_url": "",
      "post_date": "05/16/2024 04:26:44",
      "content": "<p>related:<br>\nEasyDock : Python module to automate molecular docking</p>\n<ul>\n<li><a href=\"https://github.com/ci-lab-cz/easydock\" target=\"_blank\">https://github.com/ci-lab-cz/easydock</a></li>\n<li><a href=\"https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf\" target=\"_blank\">https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf</a></li>\n</ul>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2836502,
      "author_name": "hengck23",
      "author_url": "",
      "post_date": "05/26/2024 01:03:13",
      "content": "<p><img src=\"https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F5840699370202e9e194273bbee7f9bd5%2FSelection_146.png?generation=1716685386279962&amp;alt=media\"></p>\n<p>this is useful.<br>\ni find many tutorial on docking at youtube</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2844141,
      "author_name": "hengck23",
      "author_url": "",
      "post_date": "05/30/2024 01:14:50",
      "content": "<p>grid search for AutoDock Vina:<br>\n<a href=\"https://github.com/vukoviclab/docking-scan\" target=\"_blank\">https://github.com/vukoviclab/docking-scan</a></p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2815754": "**WARNING !!!!**\nI am not a chemist. I am reading information from the wen and figuring what to do.\nIf i make any wrong steps please advise. Thanks! \n\n# [step.1: install software]  completed\n- i choose the simplest : DOCKSTRING\n- https://github.com/dockstring/dockstring\n- https://dockstring.github.io/\n- just need to install rdkit,openbabel,pymol\n- then \"python3 -m pip install dockstring\"\n- run the demo\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F10f327574b3e51ba442eed8503aec313%2FSelection_124.png?generation=1715832750604319&alt=media)\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2Fb412d2afeef25ebc42b94fbe7969a443%2FSelection_125.png?generation=1715832764139261&alt=media)\n\nscore printed is \"-11.9\". This is the value i need for my experiments later.\n\n# [step.2: prepare input files of kaggle dataset]  in progress\ni need these file for the target protein\n```\n    <name>_target.pdbqt contains the the protein structure including partial charges.\n    <name>_conf.txt contains the coordinates of the search box.\n```\n\nif you have good suggestion on how to generate these, let me know.",
    "2815759": "related:\nEasyDock : Python module to automate molecular docking\n- https://github.com/ci-lab-cz/easydock\n- https://link.springer.com/content/pdf/10.1186/s13321-023-00772-2.pdf",
    "2836502": "![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F113660%2F5840699370202e9e194273bbee7f9bd5%2FSelection_146.png?generation=1716685386279962&alt=media)\n\nthis is useful.\ni find many tutorial on docking at youtube",
    "2844141": "grid search for AutoDock Vina:\nhttps://github.com/vukoviclab/docking-scan"
  },
  "source": "meta"
}