| --- |
| license: mit |
| language: |
| - en |
| - dna |
| tags: |
| - prion |
| - dna |
| - protein |
| size_categories: |
| - 10K<n<100K |
| --- |
| |
| # prion-fasta |
|
|
| This is a collection of FASTA sequences tagged 'prion' on the US National Center for Biotechnology Information (NCBI) website. |
|
|
| ## Understanding |
|
|
| IUB/IUPAC set a format where the letters A-Z are used to represent a chain of amino acids, instead of spelling out ACGT/U of DNA and RNA. |
| Many lines of the file are accessions of [Major prion protein](https://en.wikipedia.org/wiki/Major_prion_protein) from humans and other mammals. |
| This protein is believed to normally serve a complex role in the brain and nervous system. Our current understanding is that a misfolded form of this protein |
| causes more of this protein to be folded in the same way. This misfold is transmissible to other animals, and the cause of BSE in cows, scrapie in sheep, |
| CWD in deer, a disease in camels, and CJD, vCJD, and kuru in humans. |
|
|
| ## Curation and Duplication |
|
|
| A recent biology + deep learning paper found just under 3,000 prion proteins on the UniProt database. This file contains 45,977 lines. What's going on? |
|
|
| I did limited filtering. For example proteins from a plant genome coauthored by "Florent Prion" and descriptions containing "virus" were removed. |
|
|
| Proteins such as KAH3171747.1 are from a fungus and labeled "Prion-inhibition and propagation". You can search IDs on https://www.ncbi.nlm.nih.gov if you have additional questions about specifics. |
|
|
| Some context |
| - 14,920 lines are "hypothetical protein" |
| - 4,605 are partial |
| - 2,154 are "sequence \d+ from patent" |
| - 1,342 are prion-like |
| - 392 are "Homo sapiens" |
| - 212 are peptides and |
| - 198 have the amino acid string "RIKWNRKVLPSTSQVTEARTAEIRPGAFIKQGRKLDIDFGVEGNRYYEANYWQFPDGIHYNGCS" |
|
|
| ## Prions and Deep Learning Research |
|
|
| [On Prions and Protein Design](https://press.asimov.com/articles/prions) - "Learning to use prions as nature’s laboratory for modeling protein dynamics may move us closer to mastering protein design as a whole." |
|
|
| [Deep learning reveals antimicrobial peptides within prions](https://www.nature.com/articles/s41564-026-02408-1) - "screened 19.3 million fragments from 2,897 curated prion-related proteins and identified 1,179 candidate antimicrobial peptides"; concluded "antimicrobial potential is distributed broadly across prion-associated sequence space". |
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| Their PyTorch model is somewhat old; more recent projects do finetuning by SFT or X-LoRA, and use ProGen or ESM2 as the base model. |
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