Jonathan Kenichi Ahrlind

Several multiple sequence alignment-perturbing methods enhance AlphaFold3 sampling of alternative protein states

Protein function often involves multiple conformational states. Several multiple sequence alignment-perturbing strategies, including stochastic subsampling, clustering, and column masking, have been shown to enhance AlphaFold2 (AF2) sampling of alternative protein states. Here, we evaluate these strategies on AlphaFold...