AlphaFast, a GPU-accelerated framework for AlphaFold 3 that cut single-GPU protein/ligand workloads from 10 minutes to 25 seconds.RNA was a bigger challenge. AF3 uses nhmmer for RNA MSA generation.

In AlphaFast, we added MMseqs2 nucleotide search on CPU as the default RNA path, covering Rfam, RNAcentral, and NT-RNA databases.