The reconstruction of a protein backbone from Cα coordinates

Abstract

A Monte Carlo Protein Building method to construct the backbone and Cβ atomic coordinates from known Cα coordinates is reported. The method selects values of dihedral angles from ranges established from a statistical analysis of the relationship between dihedral angles of the backbone and Cα coordinates for a protein data base. The averaged coordinates from ten backbone models of a protein were used to define a mean structure that was refined by energy minimization using the AMBER force field (GB/SA). By the latter method the average atomic deviation and rmsd of the backbone and Cβ atoms for 24 proteins is between 0.14 and 0.32 A (average 0.22 A) and 0.22 and 0.61 A (average 0.43 A), respectively. A comparison with other methods is made. © 1997 John Wiley & Sons, Inc.