An Efficient Potential For Protein Sequence Design

fined by the spatial coordinates of a subset of its atoms, usually the C # - and/or C # -atoms. A series of studies using a variety of di#erent knowledge based potentials by di#erent groups demonstrated that the energy of the native fold (i.e., putative ground state) of a sequence x can be estimated from the distribution of the values W for x in its conformation space, see e.g. [8, 4]. This allows the construction of an energy scale (z-score [5]) by which conformations of di#erent sequences can be compared: z(x, #) = W (x, #) -W (x) #W (x) . (1) Here the average energy W (x) of sequence x is obtained from evaluating x in all conformations in a dat