Stereochemical quality of protein structure coordinates

TLDR

Stereochemical quality of protein structures is evaluated using global and local parameters such as torsion angles, hydrogen bond energies, and correlations with resolution, with high‑resolution structures showing clustered distributions around ideal values. The authors aim to develop a program suite that rapidly assesses protein structures for unusual stereochemistry and potential errors. The suite computes stereochemical parameters directly from coordinate files, compares them to ideal distributions, and flags deviations. The study found that while some low‑resolution structures exhibit tightly clustered stereochemical parameters, others display abnormal scatter even at high resolution, and the derived quality measures provide a simple reliability guide beyond resolution and R‑factor.

Abstract

Abstract Methods have been developed to assess the stereochemical quality of any protein structure both globally and locally using various criteria. Several parameters can be derived from the coordinates of a given structure. Global parameters include the distribution of ϕ,ψ and χ 1 torsion angles, and hydrogen bond energies. There are clear correlations between these parameters and resolution; as the resolution improves, the distribution of the parameters becomes more clustered. These features show a broad distribution about ideal values derived from high‐resolution structures. Some structures have tightly clustered distributions even at relatively low resolutions, while others show abnormal scatter though the data go to high resolution. Additional indicators of local irregularity include proline ϕ angles, peptide bond planarities, disulfide bond lengths, and their χ 3 torsion angles. These stereochemical parameters have been used to generate measures of stereochemical quality which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution and R ‐factor. The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates. A program suite is currently being developed which will quickly check a given structure, highlighting unusual stereochemistry and possible errors.