{
  "id": 570131,
  "title": "Got a cool dataset – sharing here!",
  "url": "/competitions/stanford-rna-3d-folding/discussion/570131",
  "author_name": "MT.L",
  "post_date": "2025-03-26T01:56:19.850000",
  "votes": 12,
  "comment_count": 3,
  "views": 0,
  "content": "<p>Hey everybody,</p>\n<p>I’ve been collecting a bunch of datasets from <a href=\"https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA\" target=\"_blank\">RCSB Protein Data Bank (RCSB PDB)</a> and I’d drop them here in case they’re useful to anyone. </p>\n<p>Here are some I’ve got:<br>\n📂 <a href=\"https://www.kaggle.com/datasets/kerta27/srna3df-data-rna-glb\" target=\"_blank\">Dataset</a> - A collection of RNA Structures from <a href=\"https://www.rcsb.org/\" target=\"_blank\">RCSB PDB</a><br>\n📂 I tried <a href=\"https://www.kaggle.com/code/kerta27/standfordrna-data-extraction\" target=\"_blank\">extracting data</a> from the source and <a href=\"https://www.kaggle.com/code/kerta27/standfordrna-ribonanzanet-3d-structure-module\" target=\"_blank\">training it</a>, but it took much longer (10 minutes per epoch)</p>",
  "messages": [
    {
      "id": 3159857,
      "postDate": "2025-03-26T01:56:19.850Z",
      "content": "<p>Hey everybody,</p>\n<p>I’ve been collecting a bunch of datasets from <a href=\"https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA\" target=\"_blank\">RCSB Protein Data Bank (RCSB PDB)</a> and I’d drop them here in case they’re useful to anyone. </p>\n<p>Here are some I’ve got:<br>\n📂 <a href=\"https://www.kaggle.com/datasets/kerta27/srna3df-data-rna-glb\" target=\"_blank\">Dataset</a> - A collection of RNA Structures from <a href=\"https://www.rcsb.org/\" target=\"_blank\">RCSB PDB</a><br>\n📂 I tried <a href=\"https://www.kaggle.com/code/kerta27/standfordrna-data-extraction\" target=\"_blank\">extracting data</a> from the source and <a href=\"https://www.kaggle.com/code/kerta27/standfordrna-ribonanzanet-3d-structure-module\" target=\"_blank\">training it</a>, but it took much longer (10 minutes per epoch)</p>",
      "rawMarkdown": "Hey everybody,\n\nI’ve been collecting a bunch of datasets from [RCSB Protein Data Bank (RCSB PDB)](https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA) and I’d drop them here in case they’re useful to anyone. \n\nHere are some I’ve got:\n📂 [Dataset](https://www.kaggle.com/datasets/kerta27/srna3df-data-rna-glb) - A collection of RNA Structures from [RCSB PDB](https://www.rcsb.org/)\n📂 I tried [extracting data](https://www.kaggle.com/code/kerta27/standfordrna-data-extraction) from the source and [training it](https://www.kaggle.com/code/kerta27/standfordrna-ribonanzanet-3d-structure-module), but it took much longer (10 minutes per epoch)",
      "votes": 12
    },
    {
      "id": 3161600,
      "postDate": "2025-03-28T06:56:32.543Z",
      "content": "<p>Are you finetuning open source model or training from scratch?</p>",
      "rawMarkdown": "Are you finetuning open source model or training from scratch?\n ",
      "votes": 1,
      "replies": [
        {
          "id": 3161603,
          "postDate": "2025-03-28T07:02:07.080Z",
          "content": "<p>It's not about the model. I just downloaded all RNA structures from <a href=\"https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA\" target=\"_blank\">RCSB Protein Data Bank (RCSB PDB)</a>, as the current dataset only contains 800+ samples. More data needs to be collected from other sources.</p>",
          "rawMarkdown": "It's not about the model. I just downloaded all RNA structures from [RCSB Protein Data Bank (RCSB PDB)](https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA), as the current dataset only contains 800+ samples. More data needs to be collected from other sources."
        }
      ]
    },
    {
      "id": 3160908,
      "postDate": "2025-03-27T09:20:43.910Z",
      "rawMarkdown": "",
      "votes": 1,
      "isDeleted": true
    }
  ],
  "comments": [
    {
      "id": 3161600,
      "author_name": "Saed Bhati",
      "author_url": "",
      "post_date": "2025-03-28T06:56:32.543000",
      "content": "<p>Are you finetuning open source model or training from scratch?</p>",
      "votes": 1,
      "replies": [
        {
          "id": 3161603,
          "author_name": "MT.L",
          "author_url": "",
          "post_date": "2025-03-28T07:02:07.080000",
          "content": "<p>It's not about the model. I just downloaded all RNA structures from <a href=\"https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA\" target=\"_blank\">RCSB Protein Data Bank (RCSB PDB)</a>, as the current dataset only contains 800+ samples. More data needs to be collected from other sources.</p>",
          "votes": 0,
          "replies": []
        }
      ]
    },
    {
      "id": 3160908,
      "author_name": "",
      "author_url": "",
      "post_date": "2025-03-27T09:20:43.910000",
      "content": "",
      "votes": 1,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3159857": "Hey everybody,\n\nI’ve been collecting a bunch of datasets from [RCSB Protein Data Bank (RCSB PDB)](https://www.rcsb.org/search?q=struct_keywords.pdbx_keywords:RNA) and I’d drop them here in case they’re useful to anyone. \n\nHere are some I’ve got:\n📂 [Dataset](https://www.kaggle.com/datasets/kerta27/srna3df-data-rna-glb) - A collection of RNA Structures from [RCSB PDB](https://www.rcsb.org/)\n📂 I tried [extracting data](https://www.kaggle.com/code/kerta27/standfordrna-data-extraction) from the source and [training it](https://www.kaggle.com/code/kerta27/standfordrna-ribonanzanet-3d-structure-module), but it took much longer (10 minutes per epoch)",
    "3161600": "Are you finetuning open source model or training from scratch?\n ",
    "3160908": ""
  }
}