Accurate general method for lattice approximation of three‐dimensional structure of a chain molecule

An algorithm based on dynamic programming gives the lattice models having the minimal RMS deviations from the actual folds of protein (RNA, etc.) chains for a given lattice and a given orientation of the macromolecule relative to the lattice. The algorithm is applicable for 3‐D lattices of any kind. The accuracy of the lattice approximation increases when the distance between neighbor chain links is not rigidly fixed. Special repulsive potentials facilitate generation of self‐avoiding lattice chains. The results of model building show the efficiency and precisionof this proposed general method when compared with others. © 1995 Wiley‐Liss, Inc.