FireProt 2.0

FireProt protocol enables the automated computational design of highly stable
multiple-point mutants. FireProt 2.0 builds on top of the previously published
FireProt web, retaining the original functionality and expanding it with
several new stabilization strategies. FireProt 2.0 integrates the AlphaFold
database and the homology modelling for structure prediction, enabling
calculations starting from a sequence. Multiple-point designs are constructed using
the Bron-Kerbosch algorithm minimizing the antagonistic effect between the
individual mutations. Users can newly limit the FireProt calculation to a set
of user-defined mutations, run a saturation mutagenesis of the whole protein,
or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus
strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is
significantly faster and a reworked graphical user interface broadens the tool's
availability even to users with older hardware.