Evaluating FoldX 5.1 for MAVISp stability data collection

MAVISp (Multi-layered Assessment of VarIants by Structure for proteins) is a structure-based framework for facilitating mechanistic interpretation of missense variants, with protein stability as one of its core prediction layers. When software tools are updated, a key consideration for database curation is whether the new version can be adopted without compromising compatibility with existing entries. This study evaluated the effect of replacing FoldX 5 with FoldX 5.1 on the results of the MAVISp stability workflow. We compared predicted changes in folding free energy for 539,809 shared variants across 119 proteins. We found high overall agreement with a mean Pearson correlation of 0.933 and a mean Cohen coefficient of 0.814. Most proteins showed strong concordance, with outliers mostly explained by differences in the used protein structures between the two datasets rather than systematic inter-version bias, as mean shifts in folding free energies between versions were small. Collectively, these findings support adopting FoldX 5.1 for future MAVISp data collection. We will include a transition period, during which existing entries retain FoldX 5 annotations until their scheduled annual update, while new or updated entries are processed with FoldX 5.1. To facilitate this transition, the FoldX software version has been added as a new metadata annotation in the MAVISp database.