Summary
Conformational sampling can be achieved by AlphaFold3-generation structure prediction methods by scaling the pair representation (1). This is the part of the network that receives information from multiple sequence alignments, and is therefore somewhat equivalent to MSA subsampling.
1.
Suzuki S, Amagasa T. Steering Conformational Sampling in Boltz-2 via Pair Representation Scaling. openRxiv; 2026. Available from: https://doi.org/10.64898/2026.01.23.701250