Reconstruction of protein conformations from estimated positions of the Cα coordinates

Publisher Website
Google Scholar
Abstract
Protein Cα 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 Cα atoms. The algorithm works well for all residue types and secondary structure classes and is stable for imprecise Cα coordinates. Tests on known protein structures show that root mean square errors in predicted main‐chain and Cβ coordinates are usually less than 0.3 Å. These results are significantly more accurate than can be obtained from competing approaches, such as modeling of backbone conformations from structurally homologous fragments.