Instead of using distances, use vectors to include some directionality Sj=a(ldj-dkl b) (V-VA|+b); Can also include other information about residues i and k if desired (e.g. sequence or environment information) Si=(a+F(k)Vi- vx1l b)Instead of using distances, use vectors to include some directionality sij = a/(|dij - dkl| + b); sij = a/(|V ij - V kl| + b); Can also include other information about residues i and k if desired (e.g. sequence or environment information) sij = (a + F(i,k)/(|V ij - V kl| + b);