AlphaFold3 inference benefits more from phylogenetically diverse MSAs than deep redundant MSAs

Summary

AlphaFold3 inference shows improved performance when using phylogenetically diverse MSAs versus deep alignments dominated by near-identical sequences (1).

See also

• Diverse MSAs are better for training structure prediction neural networks than random MSAs

1.

Feldman J, Skolnick J. AlphaInterp: Mechanistic Interpretability of AlphaFold 3 Reveals How Evolutionary Information Shapes Protein Structure Prediction. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.04.22.720175