{
  "id": 574019,
  "title": "Where Can Directly Download rMSA Search Results for RNA Data from wwPDB?",
  "url": "/competitions/stanford-rna-3d-folding/discussion/574019",
  "author_name": "",
  "post_date": "2025-04-19T13:19:31.011209200Z",
  "votes": 4,
  "comment_count": 1,
  "views": 0,
  "content": "<p>the rMSA package is large (including RNAcentral, Rfam, and nt) and slow. Where can we directly download the rMSA search results corresponding to RNA data in the wwPDB?</p>",
  "messages": [
    {
      "id": "3182522",
      "postDate": "04/19/2025 13:19:31",
      "content": "<p>the rMSA package is large (including RNAcentral, Rfam, and nt) and slow. Where can we directly download the rMSA search results corresponding to RNA data in the wwPDB?</p>",
      "rawMarkdown": "the rMSA package is large (including RNAcentral, Rfam, and nt) and slow. Where can we directly download the rMSA search results corresponding to RNA data in the wwPDB?",
      "votes": null
    },
    {
      "id": "3185553",
      "postDate": "04/23/2025 13:44:32",
      "content": "<p>if you're just looking to search and align against the wwPDB entries, the PDB server's <a href=\"https://www.rcsb.org/search\" target=\"_blank\">sequence similarity search</a> is extremely fast. </p>\n<p>For your notebooks it should be straightforward to run this search offline with the relatively small set of sequences and .cif's from the PDB that have RNA, using MMseqs2: <a href=\"https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search\" target=\"_blank\">https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search</a>. </p>\n<p>Please do post here if you get a pipeline running on Kaggle that others can use!</p>",
      "rawMarkdown": "if you're just looking to search and align against the wwPDB entries, the PDB server's [sequence similarity search](https://www.rcsb.org/search) is extremely fast. \n\nFor your notebooks it should be straightforward to run this search offline with the relatively small set of sequences and .cif's from the PDB that have RNA, using MMseqs2: https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search. \n\nPlease do post here if you get a pipeline running on Kaggle that others can use!",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3185553,
      "author_name": "rhijudas",
      "author_url": "",
      "post_date": "04/23/2025 13:44:32",
      "content": "<p>if you're just looking to search and align against the wwPDB entries, the PDB server's <a href=\"https://www.rcsb.org/search\" target=\"_blank\">sequence similarity search</a> is extremely fast. </p>\n<p>For your notebooks it should be straightforward to run this search offline with the relatively small set of sequences and .cif's from the PDB that have RNA, using MMseqs2: <a href=\"https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search\" target=\"_blank\">https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search</a>. </p>\n<p>Please do post here if you get a pipeline running on Kaggle that others can use!</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "3182522": "the rMSA package is large (including RNAcentral, Rfam, and nt) and slow. Where can we directly download the rMSA search results corresponding to RNA data in the wwPDB?",
    "3185553": "if you're just looking to search and align against the wwPDB entries, the PDB server's [sequence similarity search](https://www.rcsb.org/search) is extremely fast. \n\nFor your notebooks it should be straightforward to run this search offline with the relatively small set of sequences and .cif's from the PDB that have RNA, using MMseqs2: https://www.rcsb.org/docs/search-and-browse/advanced-search/sequence-similarity-search. \n\nPlease do post here if you get a pipeline running on Kaggle that others can use!"
  },
  "source": "meta"
}