Summary
Amino acid substitution rates are dependent on the predominant rotamer in the structure (1). This could explain why MSA-based structure predictions outperform PLM-based methods, since the evolutionary information/substitution rates are passed as explicit inputs.
Figures
Ref (1)
See also
1.
Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH. Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States. Molecular Biology and Evolution. 2019;36(9):2086–103. Available from: https://doi.org/10.1093/molbev/msz122