Amino acid Changes Substitution score

Question

[muvinika]

Hi,

How do we calculate Amino acid Changes Substitution score for mutations in the gene sequences? Could you please explain about the calculation of grantham score?

Answer 1

[Ashutosh Pandey]

Here is the link to the paper

Amino Acid Difference Formula to Help Explain Protein Evolution

A formula for difference between amino acids combines properties that correlate best with protein residue substitution frequencies: composition, polarity, and molecular volume. Substitution frequencies agree much better with overall chemical difference between exchanging residues than with minimum base changes between their codons. Correlation coefficients show that fixation of mutations between dissimilar amino acids is generally rare.

In case you are looking for the code, you can modify this python code and use it: https://github.com/ashutoshkpandey/Annotation/blob/master/Grantham_score_calculator.py