THE RECONSTRUCTION OF A PROTEIN BACKBONE FROM C-ALPHA COORDINATES

A Monte Carlo Protein Building method to construct the backbone and C- beta atomic coordinates from Known C-alpha coordinates is reported. Th e method selects values of dihedral angles from ranges established fro nt a statistical analysis of the relationship between dihedral angles of the backbone and C-alpha coordinates for a protein data base. The a veraged coordinates from ten backbone models of a protein were used to define a mean structure that was refined by energy minimization risin g the AMBER force field (GB/SA). By the latter method the average atom ic deviation and rmsd of the backbone and C-beta atoms for 24 proteins is between 0.14 and 0.32 Angstrom (average 0.22 Angstrom) and 0.22 an d 0.61 Angstrom (average 0.43 Angstrom), respectively. A coinparison w ith other methods is made. (C) 1997 John Wiley & Sons, Inc.