{
  "id": 565715,
  "title": "Are context chains being considered?",
  "url": "/competitions/stanford-rna-3d-folding/discussion/565715",
  "author_name": "",
  "post_date": "2025-03-01T21:12:51.612041100Z",
  "votes": 11,
  "comment_count": 2,
  "views": 0,
  "content": "<p>I understand that the goal is to predict structure solely from the RNA sequence. However, looking for example at entry R1190 (<a href=\"https://www.rcsb.org/3d-view/7YR6)\" target=\"_blank\">https://www.rcsb.org/3d-view/7YR6)</a>, it is evident that the 3D structure may be influenced by contextual factors.</p>\n<ul>\n<li>Was this context considered by human experts when establishing the baseline?</li>\n<li>It is expected that many test sequences will not be in PDB. Will these contextual sequences be provided in the test data file?</li>\n</ul>\n<p>Thanks and congrats for rising this competition!</p>",
  "messages": [
    {
      "id": "3137699",
      "postDate": "03/01/2025 21:12:51",
      "content": "<p>I understand that the goal is to predict structure solely from the RNA sequence. However, looking for example at entry R1190 (<a href=\"https://www.rcsb.org/3d-view/7YR6)\" target=\"_blank\">https://www.rcsb.org/3d-view/7YR6)</a>, it is evident that the 3D structure may be influenced by contextual factors.</p>\n<ul>\n<li>Was this context considered by human experts when establishing the baseline?</li>\n<li>It is expected that many test sequences will not be in PDB. Will these contextual sequences be provided in the test data file?</li>\n</ul>\n<p>Thanks and congrats for rising this competition!</p>",
      "rawMarkdown": "I understand that the goal is to predict structure solely from the RNA sequence. However, looking for example at entry R1190 (https://www.rcsb.org/3d-view/7YR6), it is evident that the 3D structure may be influenced by contextual factors.\n\n- Was this context considered by human experts when establishing the baseline?\n- It is expected that many test sequences will not be in PDB. Will these contextual sequences be provided in the test data file?\n\nThanks and congrats for rising this competition!",
      "votes": null
    },
    {
      "id": "3138518",
      "postDate": "03/02/2025 16:29:48",
      "content": "<p>Good questions.<br>\n•&nbsp;Yes, the context was considered by human experts when establishing the baseline.Check out the \"Stoichiometry\" and \"Additional fields\" supplied to predictors in CASP15: <a href=\"https://predictioncenter.org/casp15/targetlist.cgi?view=rna\" target=\"_blank\">https://predictioncenter.org/casp15/targetlist.cgi?view=rna</a> <br>\n•&nbsp;Yes, information on contextual sequences will be provided in <code>all_sequences</code> in the hidden <code>test_sequences.csv</code> that your notebook will be run on for leaderboard scoring.</p>",
      "rawMarkdown": "Good questions.\n• Yes, the context was considered by human experts when establishing the baseline.Check out the \"Stoichiometry\" and \"Additional fields\" supplied to predictors in CASP15: https://predictioncenter.org/casp15/targetlist.cgi?view=rna \n• Yes, information on contextual sequences will be provided in `all_sequences` in the hidden `test_sequences.csv` that your notebook will be run on for leaderboard scoring.",
      "votes": null
    },
    {
      "id": "3138554",
      "postDate": "03/02/2025 17:23:30",
      "content": "<p>Great thanks!</p>",
      "rawMarkdown": "Great thanks!",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3138518,
      "author_name": "rhijudas",
      "author_url": "",
      "post_date": "03/02/2025 16:29:48",
      "content": "<p>Good questions.<br>\n•&nbsp;Yes, the context was considered by human experts when establishing the baseline.Check out the \"Stoichiometry\" and \"Additional fields\" supplied to predictors in CASP15: <a href=\"https://predictioncenter.org/casp15/targetlist.cgi?view=rna\" target=\"_blank\">https://predictioncenter.org/casp15/targetlist.cgi?view=rna</a> <br>\n•&nbsp;Yes, information on contextual sequences will be provided in <code>all_sequences</code> in the hidden <code>test_sequences.csv</code> that your notebook will be run on for leaderboard scoring.</p>",
      "votes": null,
      "replies": [
        {
          "id": 3138554,
          "author_name": "lbugnon",
          "author_url": "",
          "post_date": "03/02/2025 17:23:30",
          "content": "<p>Great thanks!</p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "3137699": "I understand that the goal is to predict structure solely from the RNA sequence. However, looking for example at entry R1190 (https://www.rcsb.org/3d-view/7YR6), it is evident that the 3D structure may be influenced by contextual factors.\n\n- Was this context considered by human experts when establishing the baseline?\n- It is expected that many test sequences will not be in PDB. Will these contextual sequences be provided in the test data file?\n\nThanks and congrats for rising this competition!",
    "3138518": "Good questions.\n• Yes, the context was considered by human experts when establishing the baseline.Check out the \"Stoichiometry\" and \"Additional fields\" supplied to predictors in CASP15: https://predictioncenter.org/casp15/targetlist.cgi?view=rna \n• Yes, information on contextual sequences will be provided in `all_sequences` in the hidden `test_sequences.csv` that your notebook will be run on for leaderboard scoring.",
    "3138554": "Great thanks!"
  },
  "source": "meta"
}