Body: <p>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.</p>
  <p>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 &quot;reallY&quot; identify the essential set of AAs in a given protein?
  Thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-11T20:24:15.097Z
Comments.Text: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-12T12:50:24.903Z
Comments.Text: 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
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-12T17:15:46.820Z
Comments.Text: Do you have many examples of your protein from different species? Can you look at alignments of the various homologs?
Comments.UserDisplayName: terdon
Tags: <phylogenetics><protein-structure>
Title: How to identify most important Amino Acid residues in a given protein?
ThreadText: # How to identify most important Amino Acid residues in a given protein?
  
  (Asked by: username_0 on 2022-06-11)
  
  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
  
  **Tags:** phylogenetics, protein-structure
  
  > **Comments:**
  > **username_1**: Please edit the question to limit it to a specific problem with enough detail to identify an adequate answer.  
  > **username_2**: 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  
  > **username_3**: Do you have many examples of your protein from different species? Can you look at alignments of the various homologs?  
  
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  ## 0 answers
  
  