On: The Illustrated AlphaFold

[inciampati]

It's so, so complex! I confess I had a sense of this but had no idea. We don't even hear which MSA algorithm is used to align the protein sequences.

[elanapearl → inciampati]

Hi, I was one of the authors of this! I think we briefly mentioned this in a footnote somewhere (a lot of things got cut or moved to footnotes since it is already so long & wanted to focus on the ML parts that aren't described elsewhere).

But yes as @Flobosg mentioned, for protein chains they use jackhmmer to search 4 of the databases (except when searching Uniclust30 + BFD when HHBlits is used instead) and for RNA chains they used nhmmer to search then hmmalign to re-align these to the query chain.

Hope that helps!

[flobosg → inciampati]

Input MSAs are generated with jackhmmer and HHblits and further processed, if I recall Alphafold’s paper correctly.