SSAP- Structure and Sequence Alignment Program For each pair of residues, i, assume their equivalence. How similar are their environments wrt other residues? c V E Q R R G○ A C V ik Ea/(ld -dkI b)i so s is large if d i and dk are similar Which j and i should you compare with each other? Images adapted from Taylor, WR, and CA Orengo. " Protein Structure Alignment. "J Mol Biol. 208, no. 1 (5 July 1989) 1-22SSAP - Structure and Sequence Alignment Program For each pair of residues, (i,j), assume their equivalence. How similar are their environments wrt other residues? i C A M G G k H S H R R V F E CV sik = Σa/(|dij - dkl| + b); so s is large if dij and dkl are similar. Which j and l should you compare with each other? Images adapted from Taylor, WR, and CA Orengo. "Protein Structure Alignment." J Mol Biol. 208, no. 1 (5 Jul y 1989): 1-22