{
  "id": 494749,
  "title": "Proteins databases",
  "url": "/competitions/leash-BELKA/discussion/494749",
  "author_name": "",
  "post_date": "2024-04-18T09:16:52.537513600Z",
  "votes": 2,
  "comment_count": 2,
  "views": 0,
  "content": "<p>I think provide the protein sequence to the model will increase the accuracy.<br>\nLets share some datasets that's provide protein_name and sequence to join with competition dataset</p>",
  "messages": [
    {
      "id": "2758643",
      "postDate": "04/18/2024 09:16:52",
      "content": "<p>I think provide the protein sequence to the model will increase the accuracy.<br>\nLets share some datasets that's provide protein_name and sequence to join with competition dataset</p>",
      "rawMarkdown": "I think provide the protein sequence to the model will increase the accuracy.\nLets share some datasets that's provide protein_name and sequence to join with competition dataset",
      "votes": null
    },
    {
      "id": "2758710",
      "postDate": "04/18/2024 09:58:46",
      "content": "<p>What do you mean? They have provided the exact proteins they have used:</p>\n<p>EPHX2/sEH was also screened with DELs, and hits predicted with ML approaches, in a recent study but the screening data were not published. We included EPHX2/sEH to allow contestants an external gut check for model performance by comparing to these previously-published results.</p>\n<p>We screened BRD4 purchased from Active Motif, a life sciences commercial vendor. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 44-460 from UniProt entry O60885-1, the crystal structure (for a single domain) can be found in PDB entry 7USK and predicted structure can be found in AlphaFold2 entry O60885. Additional BRD4 crystal structures with ligands bound can be found in PDB.</p>\n<p>We screened ALB purchased from Active Motif. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 25 to 609 from UniProt entry P02768, the crystal structure can be found in PDB entry 1AO6, and predicted structure can be found in AlphaFold2 entry P02768. Additional ALB crystal structures with ligands bound can be found in PDB.</p>",
      "rawMarkdown": "What do you mean? They have provided the exact proteins they have used:\n\nEPHX2/sEH was also screened with DELs, and hits predicted with ML approaches, in a recent study but the screening data were not published. We included EPHX2/sEH to allow contestants an external gut check for model performance by comparing to these previously-published results.\n\nWe screened BRD4 purchased from Active Motif, a life sciences commercial vendor. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 44-460 from UniProt entry O60885-1, the crystal structure (for a single domain) can be found in PDB entry 7USK and predicted structure can be found in AlphaFold2 entry O60885. Additional BRD4 crystal structures with ligands bound can be found in PDB.\n\nWe screened ALB purchased from Active Motif. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 25 to 609 from UniProt entry P02768, the crystal structure can be found in PDB entry 1AO6, and predicted structure can be found in AlphaFold2 entry P02768. Additional ALB crystal structures with ligands bound can be found in PDB.",
      "votes": null
    },
    {
      "id": "2801202",
      "postDate": "05/08/2024 14:42:57",
      "content": "<p>I apologize for resurrecting an old thread, but I just noticed it.  I have created a <a href=\"https://www.kaggle.com/datasets/kirkdco/leashbio-belka-proteins\" target=\"_blank\">dataset</a> with the protein structures.  Sequences can be extracted from the structures as well.</p>",
      "rawMarkdown": "I apologize for resurrecting an old thread, but I just noticed it.  I have created a [dataset](https://www.kaggle.com/datasets/kirkdco/leashbio-belka-proteins) with the protein structures.  Sequences can be extracted from the structures as well.",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2758710,
      "author_name": "gyulamaloveczky4",
      "author_url": "",
      "post_date": "04/18/2024 09:58:46",
      "content": "<p>What do you mean? They have provided the exact proteins they have used:</p>\n<p>EPHX2/sEH was also screened with DELs, and hits predicted with ML approaches, in a recent study but the screening data were not published. We included EPHX2/sEH to allow contestants an external gut check for model performance by comparing to these previously-published results.</p>\n<p>We screened BRD4 purchased from Active Motif, a life sciences commercial vendor. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 44-460 from UniProt entry O60885-1, the crystal structure (for a single domain) can be found in PDB entry 7USK and predicted structure can be found in AlphaFold2 entry O60885. Additional BRD4 crystal structures with ligands bound can be found in PDB.</p>\n<p>We screened ALB purchased from Active Motif. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 25 to 609 from UniProt entry P02768, the crystal structure can be found in PDB entry 1AO6, and predicted structure can be found in AlphaFold2 entry P02768. Additional ALB crystal structures with ligands bound can be found in PDB.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2801202,
      "author_name": "kirkdco",
      "author_url": "",
      "post_date": "05/08/2024 14:42:57",
      "content": "<p>I apologize for resurrecting an old thread, but I just noticed it.  I have created a <a href=\"https://www.kaggle.com/datasets/kirkdco/leashbio-belka-proteins\" target=\"_blank\">dataset</a> with the protein structures.  Sequences can be extracted from the structures as well.</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2758643": "I think provide the protein sequence to the model will increase the accuracy.\nLets share some datasets that's provide protein_name and sequence to join with competition dataset",
    "2758710": "What do you mean? They have provided the exact proteins they have used:\n\nEPHX2/sEH was also screened with DELs, and hits predicted with ML approaches, in a recent study but the screening data were not published. We included EPHX2/sEH to allow contestants an external gut check for model performance by comparing to these previously-published results.\n\nWe screened BRD4 purchased from Active Motif, a life sciences commercial vendor. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 44-460 from UniProt entry O60885-1, the crystal structure (for a single domain) can be found in PDB entry 7USK and predicted structure can be found in AlphaFold2 entry O60885. Additional BRD4 crystal structures with ligands bound can be found in PDB.\n\nWe screened ALB purchased from Active Motif. For those contestants wishing to incorporate protein structural information in their submissions, the amino acid sequence is positions 25 to 609 from UniProt entry P02768, the crystal structure can be found in PDB entry 1AO6, and predicted structure can be found in AlphaFold2 entry P02768. Additional ALB crystal structures with ligands bound can be found in PDB.",
    "2801202": "I apologize for resurrecting an old thread, but I just noticed it.  I have created a [dataset](https://www.kaggle.com/datasets/kirkdco/leashbio-belka-proteins) with the protein structures.  Sequences can be extracted from the structures as well."
  },
  "source": "meta"
}