10 ms·

As an ex biomedical researcher I was trying to think what protein I should enter and see, and couldn't come up with a protein that I know of, that didn't have a

As an ex biomedical researcher I was trying to think what protein I should enter and see, and couldn't come up with a protein that I know of, that didn't have a structure already (at least a crude one). That is, we roughly know how most known important proteins look like. This is an amazing tool, and will he indispensable in labs (I'll expect any lab to use this site at least once a year?) But it's not as transformative as some might think.

amelius 5y ago
https://www.embl.org/news/science/alphafold-potential-impacts/ https://www.embl.org/news/science/alphafold-potential-impact... > A discussion of the applications that AlphaFold DB may enable and the possible impact of the resource on science and society
pelorat 5y ago
Do we really know the structure of every protein that assembles into a human cell?
- seventytwo 5y ago
  Definitely not.
- _RPL5_ 5y ago
  From their abstract: --- After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally-determined structure1. Here we dramatically expand structural coverage by applying the state-of-the-art machine learning method, AlphaFold2, at scale to almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. https://www.nature.com/articles/s41586-021-03828-1 https://www.nature.com/articles/s41586-021-03828-1 --- The metric they use (residues) is a bit unusual (I would have used number of proteins instead), but I assume they wanted to account for ambiguity (such as proteins with partial structures).
- cing 5y ago
  One of the reasons we don't have them all is that individual genes can encode for multiple protein isoforms through alternative splicing. AlphaFold was only run on one. Otherwise, there's lots of important biochemical/biophysical processes that impact structure, as cells are only about 50% protein by weight.

amelius 5y ago

https://www.embl.org/news/science/alphafold-potential-impacts/ https://www.embl.org/news/science/alphafold-potential-impact... > A discussion of the applications that AlphaFold DB may enable and the possible impact of the resource on science and society

pelorat 5y ago

Do we really know the structure of every protein that assembles into a human cell?

seventytwo 5y ago
Definitely not.
_RPL5_ 5y ago
From their abstract: --- After decades of effort, 17% of the total residues in human protein sequences are covered by an experimentally-determined structure1. Here we dramatically expand structural coverage by applying the state-of-the-art machine learning method, AlphaFold2, at scale to almost the entire human proteome (98.5% of human proteins). The resulting dataset covers 58% of residues with a confident prediction, of which a subset (36% of all residues) have very high confidence. https://www.nature.com/articles/s41586-021-03828-1 https://www.nature.com/articles/s41586-021-03828-1 --- The metric they use (residues) is a bit unusual (I would have used number of proteins instead), but I assume they wanted to account for ambiguity (such as proteins with partial structures).
cing 5y ago
One of the reasons we don't have them all is that individual genes can encode for multiple protein isoforms through alternative splicing. AlphaFold was only run on one. Otherwise, there's lots of important biochemical/biophysical processes that impact structure, as cells are only about 50% protein by weight.