Reconstruction of protein conformations from estimated positions of the C alpha coordinates.

Protein C alpha coordinates are used to accurately reconstruct complete protein backbones and side-chain directions. This work employs potentials of mean force to align semirigid peptide groups around the axes that connect successive C alpha atoms. The algorithm works well for all residue types and secondary structure classes and is stable for imprecise C alpha coordinates. Tests on known protein structures show that root mean square errors in predicted main-chain and C beta coordinates are usually less than 0.3 A. These results are significantly more accurate than can be obtained from competing approaches, such as modeling of backbone conformations from structurally homologous fragments.