{ "id": 565426, "title": "Step 1 : Literature Review - Related Research Papers", "url": "/competitions/stanford-rna-3d-folding/discussion/565426", "author_name": "", "post_date": "2025-02-28T12:28:47.213464800Z", "votes": 21, "comment_count": 3, "views": 0, "content": "

Hey, there! Sharing a few related papers that might help everybody moving forward. Good luck! :))

\n
    \n
  1. Ribonanza: deep learning of RNA structure through dual crowdsourcing.
    2. \n
  2. gRNAde: Geometric Deep Learning for 3D RNA inverse design
    3. \n
  3. A Method to Predict the 3D Structure of an RNA Scaffold
    4. \n
  4. trRosettaRNA: automated prediction of RNA 3D structure with transformer network
    5. \n
  5. Accurate RNA 3D structure prediction using a language model-based deep learning approach\n
    6. \n
  6. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks
    7. \n
  7. RNA 3D Structure Prediction: Progress and Perspective
    8. \n
  8. RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling
    9. \n
  9. Predicting the 3D Structure of RNA from Sequence
    10. \n
  10. Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data\n
    11. \n
", "messages": [ { "id": "3136346", "postDate": "02/28/2025 12:28:47", "content": "

Hey, there! Sharing a few related papers that might help everybody moving forward. Good luck! :))

\n
    \n
  1. Ribonanza: deep learning of RNA structure through dual crowdsourcing.
    2. \n
  2. gRNAde: Geometric Deep Learning for 3D RNA inverse design
    3. \n
  3. A Method to Predict the 3D Structure of an RNA Scaffold
    4. \n
  4. trRosettaRNA: automated prediction of RNA 3D structure with transformer network
    5. \n
  5. Accurate RNA 3D structure prediction using a language model-based deep learning approach\n
    6. \n
  6. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks
    7. \n
  7. RNA 3D Structure Prediction: Progress and Perspective
    8. \n
  8. RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling
    9. \n
  9. Predicting the 3D Structure of RNA from Sequence
    10. \n
  10. Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data\n
    11. \n
", "rawMarkdown": "Hey, there! Sharing a few related papers that might help everybody moving forward. Good luck! :))\n\n1. [Ribonanza: deep learning of RNA structure through dual crowdsourcing](https://pmc.ncbi.nlm.nih.gov/articles/PMC10925082/).\n2. [gRNAde: Geometric Deep Learning for 3D RNA inverse design](https://arxiv.org/html/2305.14749v4)\n3. [A Method to Predict the 3D Structure of an RNA Scaffold](https://pmc.ncbi.nlm.nih.gov/articles/PMC5512611/#:~:text=To%20predict%20RNA%203D%20structures,predicts%20the%20corresponding%203D%20structures.)\n4. [trRosettaRNA: automated prediction of RNA 3D structure with transformer network](https://www.nature.com/articles/s41467-023-42528-4)\n5. [Accurate RNA 3D structure prediction using a language model-based deep learning approach\n](https://www.nature.com/articles/s41592-024-02487-0)\n6. [Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks](https://pubmed.ncbi.nlm.nih.gov/37838833/)\n7. [RNA 3D Structure Prediction: Progress and Perspective](https://www.mdpi.com/1420-3049/28/14/5532)\n8. [RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling ](https://academic.oup.com/nar/article/51/7/3341/7067938)\n9. [Predicting the 3D Structure of RNA from Sequence](https://link.springer.com/referenceworkentry/10.1007/978-981-16-1313-5_14-1)\n10. [Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data\n](https://www.cell.com/structure/fulltext/S0969-2126(24)00332-0)", "votes": null }, { "id": "3136362", "postDate": "02/28/2025 12:44:33", "content": "

Wow, thanks for sharing such a great list of resources, @ahsuna123 ! These papers look incredibly helpful for anyone diving into RNA structure research or understanding the background behind this competition. I love how collaborative this feels—wishing everyone tons of luck with their Submissions :)

", "rawMarkdown": "Wow, thanks for sharing such a great list of resources, @ahsuna123 ! These papers look incredibly helpful for anyone diving into RNA structure research or understanding the background behind this competition. I love how collaborative this feels—wishing everyone tons of luck with their Submissions :)", "votes": null }, { "id": "3160536", "postDate": "03/26/2025 22:15:08", "content": "

This is useful for beginners.

", "rawMarkdown": "This is useful for beginners.", "votes": null }, { "id": "3168989", "postDate": "04/03/2025 02:37:06", "content": "

Thank you so much! I'm now deeply focused on researching for this competition.

", "rawMarkdown": "Thank you so much! I'm now deeply focused on researching for this competition.", "votes": null } ], "comments": [ { "id": 3136362, "author_name": "keyushnisar", "author_url": "", "post_date": "02/28/2025 12:44:33", "content": "

Wow, thanks for sharing such a great list of resources, @ahsuna123 ! These papers look incredibly helpful for anyone diving into RNA structure research or understanding the background behind this competition. I love how collaborative this feels—wishing everyone tons of luck with their Submissions :)

", "votes": null, "replies": [] }, { "id": 3160536, "author_name": "", "author_url": "", "post_date": "03/26/2025 22:15:08", "content": "

This is useful for beginners.

", "votes": null, "replies": [] }, { "id": 3168989, "author_name": "hvanphucs112", "author_url": "", "post_date": "04/03/2025 02:37:06", "content": "

Thank you so much! I'm now deeply focused on researching for this competition.

", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "3136346": "Hey, there! Sharing a few related papers that might help everybody moving forward. Good luck! :))\n\n1. [Ribonanza: deep learning of RNA structure through dual crowdsourcing](https://pmc.ncbi.nlm.nih.gov/articles/PMC10925082/).\n2. [gRNAde: Geometric Deep Learning for 3D RNA inverse design](https://arxiv.org/html/2305.14749v4)\n3. [A Method to Predict the 3D Structure of an RNA Scaffold](https://pmc.ncbi.nlm.nih.gov/articles/PMC5512611/#:~:text=To%20predict%20RNA%203D%20structures,predicts%20the%20corresponding%203D%20structures.)\n4. [trRosettaRNA: automated prediction of RNA 3D structure with transformer network](https://www.nature.com/articles/s41467-023-42528-4)\n5. [Accurate RNA 3D structure prediction using a language model-based deep learning approach\n](https://www.nature.com/articles/s41592-024-02487-0)\n6. [Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks](https://pubmed.ncbi.nlm.nih.gov/37838833/)\n7. [RNA 3D Structure Prediction: Progress and Perspective](https://www.mdpi.com/1420-3049/28/14/5532)\n8. [RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling ](https://academic.oup.com/nar/article/51/7/3341/7067938)\n9. [Predicting the 3D Structure of RNA from Sequence](https://link.springer.com/referenceworkentry/10.1007/978-981-16-1313-5_14-1)\n10. [Advances in the field of RNA 3D structure prediction and modeling, with purely theoretical approaches, and with the use of experimental data\n](https://www.cell.com/structure/fulltext/S0969-2126(24)00332-0)", "3136362": "Wow, thanks for sharing such a great list of resources, @ahsuna123 ! These papers look incredibly helpful for anyone diving into RNA structure research or understanding the background behind this competition. I love how collaborative this feels—wishing everyone tons of luck with their Submissions :)", "3160536": "This is useful for beginners.", "3168989": "Thank you so much! I'm now deeply focused on researching for this competition." }, "source": "meta" }