The reconstruction of side-chain conformations from protein Cα coordinates

A model of nine proteins including side-chain atoms have been built from the known C^α coordinates and amino acid sequences using a Monte Carlo Protein Building Annealing method. The Cartesian coordinates for the side-chain atoms were established with bond lengths and angles selected randomly from within previously determined ranges. A simulated annealing technique is used to generate some 300 structures with differing side-chain conformations. The atomic coordinates of the backbone atoms are fixed during the simulated annealing process. The coordinates of the side-chain atoms of 300 low energy conformations are averaged to obtain a mean structure that is minimized with the C^α atoms constrained to their position in the x-ray structure using the OPLS/AMBER force field with the GB/SA water model. The rms deviation of the main-chain atoms (without C^β) compared with the corresponding crystal structures is in the range 0.20–0.64 Å. The rms deviation of the side-chain atoms is between 1.72 and 2.71 Å and for all atoms is between 1.19 and 1.99 Å. The method is insensitive to random errors in the C^α positions and the computational requirement is modest. © 1997 John Wiley & Sons, Inc.