Comment by flobosg

2 years ago

> AlphaFold is amazing homology modeling

If it is homology modelling, then how can it work without input template structures?

8 comments

flobosg

It has template structures. AlphaFold uses the following databases:

    BFD,
    MGnify,
    PDB70,
    PDB (structures in the mmCIF format),
    PDB seqres – only for AlphaFold-Multimer,
    Uniclust30,
    UniProt – only for AlphaFold-Multimer,
    UniRef90.

flobosg 2 years ago
Those databases are used to derive the evolutionary couplings and distance matrices used by the algorithm. Several of those databases aren’t even structural ones. Furthermore, AlphaFold can function with only a MSA as an input, without retrieving a single PDB coordinate.
- COGlory 2 years ago
  
  It's all about boosting signal by finding other proteins that are similar, until you get to the point that you can identify a fold to assign to a region of the protein. That's why some are structural, and some are not.
  >Furthermore, AlphaFold can function with only a MSA as an input, without retrieving a single PDB coordinate.
  Yes, it has a very nice model of what sequences should look like in 3D. That model is derived from experimental data. So if I give AlphaFold an MSA of a new, unknown protein fold (substantively away from any known fold), it cannot predict it.
  
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