{
  "id": 568379,
  "title": "TM score Lalign",
  "url": "/competitions/stanford-rna-3d-folding/discussion/568379",
  "author_name": "",
  "post_date": "2025-03-15T14:05:40.567584200Z",
  "votes": null,
  "comment_count": 2,
  "views": 0,
  "content": "<p>Can anyone please tell me briefly how is Lalign counted in the formula that is given (TM-score) and what is the thresh hold for a residue to align with the ground truth residue. </p>",
  "messages": [
    {
      "id": "3150451",
      "postDate": "03/15/2025 14:05:40",
      "content": "<p>Can anyone please tell me briefly how is Lalign counted in the formula that is given (TM-score) and what is the thresh hold for a residue to align with the ground truth residue. </p>",
      "rawMarkdown": "Can anyone please tell me briefly how is Lalign counted in the formula that is given (TM-score) and what is the thresh hold for a residue to align with the ground truth residue.",
      "votes": null
    },
    {
      "id": "3150636",
      "postDate": "03/15/2025 17:19:36",
      "content": "<p>there is no fixed cutoff or threshold, a residue <code>10Å</code> away can be aligned if it’s the \"least bad\" option for the collective score. </p>\n<p>collective score is decided by the US-align algorithm, which also decides the L_align residues</p>\n<p>collective score is the TM-Score </p>",
      "rawMarkdown": "there is no fixed cutoff or threshold, a residue `10Å` away can be aligned if it’s the \"least bad\" option for the collective score. \n\n\ncollective score is decided by the US-align algorithm, which also decides the L_align residues\n\ncollective score is the TM-Score",
      "votes": null
    },
    {
      "id": "3151149",
      "postDate": "03/16/2025 10:55:15",
      "content": "<p>Thank you so much for the explanation, just to get things inline the whole score is calculated by the command(US-align) the only thing we have to do is to input the PDB fomats of the ground truth and prdicted atoms into it.(I have come to this conclusion after checking out the \"<em>Ribonanza TM-Score</em>\") </p>",
      "rawMarkdown": "Thank you so much for the explanation, just to get things inline the whole score is calculated by the command(US-align) the only thing we have to do is to input the PDB fomats of the ground truth and prdicted atoms into it.(I have come to this conclusion after checking out the \"*Ribonanza TM-Score*\")",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 3150636,
      "author_name": "jaejohn",
      "author_url": "",
      "post_date": "03/15/2025 17:19:36",
      "content": "<p>there is no fixed cutoff or threshold, a residue <code>10Å</code> away can be aligned if it’s the \"least bad\" option for the collective score. </p>\n<p>collective score is decided by the US-align algorithm, which also decides the L_align residues</p>\n<p>collective score is the TM-Score </p>",
      "votes": null,
      "replies": [
        {
          "id": 3151149,
          "author_name": "niteesg859",
          "author_url": "",
          "post_date": "03/16/2025 10:55:15",
          "content": "<p>Thank you so much for the explanation, just to get things inline the whole score is calculated by the command(US-align) the only thing we have to do is to input the PDB fomats of the ground truth and prdicted atoms into it.(I have come to this conclusion after checking out the \"<em>Ribonanza TM-Score</em>\") </p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "3150451": "Can anyone please tell me briefly how is Lalign counted in the formula that is given (TM-score) and what is the thresh hold for a residue to align with the ground truth residue.",
    "3150636": "there is no fixed cutoff or threshold, a residue `10Å` away can be aligned if it’s the \"least bad\" option for the collective score. \n\n\ncollective score is decided by the US-align algorithm, which also decides the L_align residues\n\ncollective score is the TM-Score",
    "3151149": "Thank you so much for the explanation, just to get things inline the whole score is calculated by the command(US-align) the only thing we have to do is to input the PDB fomats of the ground truth and prdicted atoms into it.(I have come to this conclusion after checking out the \"*Ribonanza TM-Score*\")"
  },
  "source": "meta"
}