Hello experts in residue coevolution analysis of proteins,
I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein. The issue is that rather than having a Multiple Sequence Alignment (MSA) which is used as an input by the relevant tools (e.g. evcouplings), I have position wise preferences for 20 amino acids for the protein.
For the protein with length
L, I have a
20*L matrix of position-wise preferences for amino acids.
I would like to use this matrix as a direct input for coevolution analysis.
Would it be possible to calculate the residue coevolution direcly from a residue preference matrix?
Any recommendation for a method of choice or a software tool would be helpful.