Fig. 2

Analysis of evolutionary couplings. Starting from a given WT protein amino acid sequence, we apply Sibe to estimate the site bias of and pairwise couplings between amino acids as a statistical potential for protein design in silico. and a bias energy function (residue-contact) in protein folding. a Detection of covariations (e.g., at the ith and jth positions colored in orange) and conserved amino acids (e.g., positions colored in dark red) from the multiple sequence alignment of N sequences by L positions obtained by searching the WT sequence against the sequence database. b Analysis on the detected coupled and conserved amino acids results in an interaction potential. c residue blocks were achieved by independent component analysis and highlight each of them may have a distinct functional role in the protein family