How to model a truncated protein

Question

[nkabo]

Hello,

I am working on modelling a truncated protein (E520* for example) due to a stop-gain mutation. I am trying to show how the protein structure changes and I need to calculate back-bone root-mean-square deviations (RMSD), average Ca root-mean-square fluctuations (RMSF) etc. I am familiar with the methods for amino acid substitutions, however I have no experience in modelling a truncated protein.

Would it make sense if I try modelling the structure in AlphaFold or SWISS-MODEL based on FASTA sequence of first 519 aminoacids for example? But as far as I know, these methods do not provide the calculations mentioned above. Could you suggest a solution?

Thanks a lot