Lattice modeling: Accuracy of energy calculations

Energy calculations based on lattice models of protein chains are always approximate, because any such a model distorts distances between chain links and, consequently, the energies of interaction between them. The energetic errors of lattice models are examined here for 15 proteins of different sizes and types of secondary structure, for lattice spacings ranging from 0.25 to 2.5 Å. The lattice models are derived using previously described algorithms which insure a minimal root mean square (rms) deviation from the off-lattice structure for any given lattice-protein orientation. For each protein structure we computed a set of different lattice models with virtually equal rms deviations, and then compared their energies. Energy calculations were based on the pairwise potentials. We found that the energies of lattice models follows a normal distribution with a nonnegligible dispersion, even at a fine lattice spacing of 0.25 Å. For any lattice model of a protein, the lattice spacing must be 1.0 Å or less in order to be able to distinguish energetically between the folded and extended states. However, when an ensemble of lattice models is considered, this distinction can be made for lattice spacing up to 2.0 Å. We conclude that to attain a better approximation of the protein lattice model energies, one must adjust potentials to the lattice spacing. © 1996 by John Wiley & Sons, Inc.