Dear Akshay Shirsath

it depends if there is a PDB structure avaialble you can use softwares that calculate the energy changes induced by aminoacid replacment. I the past i used the Popmusic program (https://soft.dezyme.com/) and it works quite well.

If there is not structure avaialble, the prediction is much more difficult.

°One think that you can try is check how the mutation can change the prediction of the secondary structure of the protein, because a mutation that is predicted to destabilize a stable secondary strcture region as alpha-elix or Beta-shhet can have certanilly more important effect than a mutation that seems to do not alter it.

to calculate 2ndari structures i'm generally using the

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_secco%20ns.html

which allow to use in parallel different algoritms.

good luck

Manuele

You could try AlphaFold2 if you are after looking for changes in structure.