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This work determines the activation pathway of hHV1, together with structural models of its resting and activated states, using an approach that integrates all-atom continuous constant-pH MD (CpHMD), weighted-ensemble (THE AUTHORS) path sampling, and AlphaFold modeling.
It is shown that increased sampling and AlphaFold3 generally improve performance relative to default sampling and AlphaFold2, however predictive accuracy and improvement levels varied considerably among interface classes, with antibody-peptide complexes representing a challenge despite their small antigen size.
A systematic NMR-characterized dataset of mutants of the GA/GB model fold-switching system is presented and it is found that this benchmark revealed variable and position-dependent performance across methods, with certain AlphaFold2-based algorithms able to predict mutant effects at individual sites, indicating some un...
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