Summary
AlphaFold3-generation methods like Boltz and Chai exclusively incorporate MSA information into the pair representation, in contrast with Evoformer-based methods that reason over the information in the folding trunk (1).
1.
Abramson J, Adler J, Dunger J, Evans R, Green T, Pritzel A, et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 2024;630(8016):493–500. Available from: https://doi.org/10.1038/s41586-024-07487-w