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Continuing from the title, in my context, important means that changing the set of AAs (either or one more many) changes the domain and/or fold and/or function and/or family etc.

I noticed that there are two types of methods Protbert (protein language models, sequence-based methods) and/or Alphafold (structure (tertiary) based methods); one needs both methods to "reallY" identify the essential set of AAs in a given protein? Thanks

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    $\begingroup$ Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer. $\endgroup$
    – Community Bot
    Jun 11, 2022 at 20:24
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    $\begingroup$ Sorry. This question is ill posed as it completely depends on context —namely is simply a question of what are the main roles AA residues can take. Core residues when mutated may cause and increase in Gibbs free energy of folding (i.e. less energy is released when folded from a magically linear protein form), these are key to Structure as seen in PDB and predicted by Alphafold. Catalytic residues are key to activity. Channel gate residues are key to permeability. etc etc etc etc $\endgroup$
    – Matteo Ferla
    Jun 12, 2022 at 12:50
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    $\begingroup$ Do you have many examples of your protein from different species? Can you look at alignments of the various homologs? $\endgroup$
    – terdon ♦
    Jun 12, 2022 at 17:15

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