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as-cle-bert 
posted an update May 23
Post
1401
Hi HF Community!🤗

If you are excited about AlphaFold3, but upset because it is not open-source, I might have a solution to cheer you up a little bit:

as-cle-bert/proteinviz

This is a space that lets you predict the 3D structure of proteins from their amino-acidic sequences, with the protein folding model facebook/esmfold_v1: using this space is the perfect quick-start to become a Protein Scientist! (or maybe not, who knows...🤔)

In the meantime, if you are curious about what's going on with AlphaFold3 and want something Biologist🔬/Computer Scientist💻-friendly, you can also check out the latest community blog post I wrote: https://huggingface.co/blog/as-cle-bert/what-is-going-on-with-alphafold3 🚀

Have fun and enjoy open-source science!🧬
lunarflu

really love the visual feedback from it!
image.png

maybe for some further suggestions coming from a non-protein-expert:

  • which letters are valid for using in proteins?
  • maybe some preset examples people can click to understand instantly how it works?
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as-cle-bert
•
edited May 23

Hi @lunarflu , thanks for the feedback!

So, to reply to your questions:

  • There are 20 amino-acids (represented by letters) that one can use + some rare or degenerate (meaning you are unsure what letter to put) ones. You can find them here: https://bredagenetics.com/amino-acid-codes-symbols/
  • I did not think of that, but I'll sure do :)) Thank you very much for the suggestion!

In the meanwhile, if you are interested in some example proteins to try out, I suggest using Uniprot and searching for some proteins like "Insulin", "Beta-lactamase" or "Hemoglobin". There should be the amino-acidic sequence and the actual 3D structure that you can compare!

introvoyz041

Congratulations! Thank you with your new hf space. I've tried your space with other hf space and found out that fostamatinib can effectively inhibit breast cancer cells.

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as-cle-bert

That's fantastic! Would be glad to hear more about your research!🤗

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