{ "id": 411409, "title": "The spatial structure of amino acids", "url": "/competitions/cafa-5-protein-function-prediction/discussion/411409", "author_name": "", "post_date": "2023-05-19T04:43:35.513481300Z", "votes": 7, "comment_count": 6, "views": 0, "content": "

Spatial structure is an important factor affecting function.

\n

So I tried to predict the spatial structure of P20536 using AlphaFold.
\nHowever the prediction took too long to be realistic….
\nIt would take a lot of computing power to do that, but I'm just a noob.

\n

Here is the pdb file

\n

\"\"

\n

\"\"

\n

\"\"

", "messages": [ { "id": "2265210", "postDate": "05/19/2023 04:43:35", "content": "

Spatial structure is an important factor affecting function.

\n

So I tried to predict the spatial structure of P20536 using AlphaFold.
\nHowever the prediction took too long to be realistic….
\nIt would take a lot of computing power to do that, but I'm just a noob.

\n

Here is the pdb file

\n

\"\"

\n

\"\"

\n

\"\"

", "rawMarkdown": "Spatial structure is an important factor affecting function.\n\nSo I tried to predict the spatial structure of P20536 using AlphaFold.\nHowever the prediction took too long to be realistic....\nIt would take a lot of computing power to do that, but I'm just a noob.\n\nHere is the [**pdb**](https://www.kaggle.com/datasets/horikitasaku/p20536) file\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2Fcadda09f226158047e92eb845b5ed586%2FHTTPS___FILE2B.VSCODE-RESOURCE.VSCODE-CDN.NET_D3A_CODE_KAGGLE_CAFA_PROTEIN_P20536.PDB.png?generation=1684471170068295&alt=media)\n\n\n ![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2F3b58f6013a0f49cad20916043114cf01%2FFwdvMHVaMAEabqN.jpg?generation=1684471493510393&alt=media)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2F709b02fecf48a9e870ca3d6cd4558a8d%2FFwdwianagAQA2vo.jpg?generation=1684471548271719&alt=media)", "votes": null }, { "id": "2265321", "postDate": "05/19/2023 06:50:52", "content": "

I haven't checked if all of the test/train proteins are covered, but there is a database of precomputed AlphaFold2 structures.

\n

Link: https://alphafold.ebi.ac.uk/

", "rawMarkdown": "I haven't checked if all of the test/train proteins are covered, but there is a database of precomputed AlphaFold2 structures.\n\nLink: https://alphafold.ebi.ac.uk/", "votes": null }, { "id": "2265336", "postDate": "05/19/2023 07:11:35", "content": "

Thank you for reminding me!
\nRight! I did find some genes, but many were missing, such as the example I posted \"P20536\".

", "rawMarkdown": "Thank you for reminding me!\nRight! I did find some genes, but many were missing, such as the example I posted \"P20536\".", "votes": null }, { "id": "2265983", "postDate": "05/19/2023 16:12:14", "content": "

Other resources that include experimental and predicted structures, including classification:

\n

http://www.cathdb.info/

\n

https://www.rcsb.org/

", "rawMarkdown": "Other resources that include experimental and predicted structures, including classification:\n\nhttp://www.cathdb.info/\n\nhttps://www.rcsb.org/", "votes": null }, { "id": "2266473", "postDate": "05/20/2023 05:29:11", "content": "

Thank you for sharing! I'll try!

", "rawMarkdown": "Thank you for sharing! I'll try!", "votes": null }, { "id": "2270022", "postDate": "05/22/2023 23:01:17", "content": "

There are plenty of available protein structures that are likely to be very similar to that one:

\n

https://www.uniprot.org/uniprotkb/P20995/entry#structure

\n

http://www.cathdb.info/version/latest/superfamily/3.40.470.10

\n

Even where AlphaFold structural models aren't available for a specific sequence, homolog structures may already exist.

", "rawMarkdown": "There are plenty of available protein structures that are likely to be very similar to that one:\n\n[https://www.uniprot.org/uniprotkb/P20995/entry#structure](https://www.uniprot.org/uniprotkb/P20995/entry#structure)\n\n[http://www.cathdb.info/version/latest/superfamily/3.40.470.10](http://www.cathdb.info/version/latest/superfamily/3.40.470.10)\n\nEven where AlphaFold structural models aren't available for a specific sequence, homolog structures may already exist.", "votes": null }, { "id": "2270047", "postDate": "05/23/2023 00:10:28", "content": "

You're absolutely right!
\nI soon realized this. It was not predicted by alphafold because of the experimentally discovered structure.

", "rawMarkdown": "You're absolutely right!\nI soon realized this. It was not predicted by alphafold because of the experimentally discovered structure.", "votes": null } ], "comments": [ { "id": 2265321, "author_name": "norixmb", "author_url": "", "post_date": "05/19/2023 06:50:52", "content": "

I haven't checked if all of the test/train proteins are covered, but there is a database of precomputed AlphaFold2 structures.

\n

Link: https://alphafold.ebi.ac.uk/

", "votes": null, "replies": [ { "id": 2265336, "author_name": "horikitasaku", "author_url": "", "post_date": "05/19/2023 07:11:35", "content": "

Thank you for reminding me!
\nRight! I did find some genes, but many were missing, such as the example I posted \"P20536\".

", "votes": null, "replies": [ { "id": 2265983, "author_name": "iddux1", "author_url": "", "post_date": "05/19/2023 16:12:14", "content": "

Other resources that include experimental and predicted structures, including classification:

\n

http://www.cathdb.info/

\n

https://www.rcsb.org/

", "votes": null, "replies": [ { "id": 2266473, "author_name": "horikitasaku", "author_url": "", "post_date": "05/20/2023 05:29:11", "content": "

Thank you for sharing! I'll try!

", "votes": null, "replies": [] } ] }, { "id": 2270022, "author_name": "jbomitchell", "author_url": "", "post_date": "05/22/2023 23:01:17", "content": "

There are plenty of available protein structures that are likely to be very similar to that one:

\n

https://www.uniprot.org/uniprotkb/P20995/entry#structure

\n

http://www.cathdb.info/version/latest/superfamily/3.40.470.10

\n

Even where AlphaFold structural models aren't available for a specific sequence, homolog structures may already exist.

", "votes": null, "replies": [ { "id": 2270047, "author_name": "horikitasaku", "author_url": "", "post_date": "05/23/2023 00:10:28", "content": "

You're absolutely right!
\nI soon realized this. It was not predicted by alphafold because of the experimentally discovered structure.

", "votes": null, "replies": [] } ] } ] } ] } ], "raw_markdown_by_id": { "2265210": "Spatial structure is an important factor affecting function.\n\nSo I tried to predict the spatial structure of P20536 using AlphaFold.\nHowever the prediction took too long to be realistic....\nIt would take a lot of computing power to do that, but I'm just a noob.\n\nHere is the [**pdb**](https://www.kaggle.com/datasets/horikitasaku/p20536) file\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2Fcadda09f226158047e92eb845b5ed586%2FHTTPS___FILE2B.VSCODE-RESOURCE.VSCODE-CDN.NET_D3A_CODE_KAGGLE_CAFA_PROTEIN_P20536.PDB.png?generation=1684471170068295&alt=media)\n\n\n ![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2F3b58f6013a0f49cad20916043114cf01%2FFwdvMHVaMAEabqN.jpg?generation=1684471493510393&alt=media)\n\n![](https://www.googleapis.com/download/storage/v1/b/kaggle-forum-message-attachments/o/inbox%2F11676771%2F709b02fecf48a9e870ca3d6cd4558a8d%2FFwdwianagAQA2vo.jpg?generation=1684471548271719&alt=media)", "2265321": "I haven't checked if all of the test/train proteins are covered, but there is a database of precomputed AlphaFold2 structures.\n\nLink: https://alphafold.ebi.ac.uk/", "2265336": "Thank you for reminding me!\nRight! I did find some genes, but many were missing, such as the example I posted \"P20536\".", "2265983": "Other resources that include experimental and predicted structures, including classification:\n\nhttp://www.cathdb.info/\n\nhttps://www.rcsb.org/", "2266473": "Thank you for sharing! I'll try!", "2270022": "There are plenty of available protein structures that are likely to be very similar to that one:\n\n[https://www.uniprot.org/uniprotkb/P20995/entry#structure](https://www.uniprot.org/uniprotkb/P20995/entry#structure)\n\n[http://www.cathdb.info/version/latest/superfamily/3.40.470.10](http://www.cathdb.info/version/latest/superfamily/3.40.470.10)\n\nEven where AlphaFold structural models aren't available for a specific sequence, homolog structures may already exist.", "2270047": "You're absolutely right!\nI soon realized this. It was not predicted by alphafold because of the experimentally discovered structure." }, "source": "meta" }