Efficient algorithm for the reconstruction of a protein backbone from the α‐carbon coordinates

Abstract

Abstract We present an analytical method for generating a whole protein backbone structure from the coordinates of the α‐carbons. The procedure begins by automatically positioning the β‐carbons for every residue, and then the positions of the carbonyl groups and the amide nitrogens are also computed. The method is based upon the simultaneous minimization of a number of geometrical constraints that appear in real proteins and that can be very easily formulated as a set of trigonometric relations between the coordinates of the atoms involved in the backbone reconstruction. The resulting algorithm has been tested for proteins of very different sizes and topologies, and can advantageously compete with other methods proposed for this goal both in accuracy and in computational requirements. Possible ways of further refinement of the resulting structures are discussed.