Stereochemical quality of protein structure coordinates

Area of Science:

• Structural Biology
• Biochemistry
• Computational Biology

Background:

• Protein structure quality is crucial for biological interpretation.
• Assessing stereochemical integrity is essential for validating experimental structures.
• Existing metrics like resolution and R-factor have limitations in fully capturing structural quality.

Purpose of the Study:

• To develop and present methods for evaluating the stereochemical quality of protein structures.
• To establish global and local criteria for assessing structural reliability.
• To provide a complementary measure to resolution and R-factor for structure validation.

Main Methods:

• Deriving global parameters from protein coordinates, including phi, psi, and chi 1 torsion angle distributions.
• Analyzing hydrogen bond energies as a global indicator of stereochemical quality.
• Identifying local irregularities using parameters such as proline phi angles, peptide bond planarity, and disulfide bond geometry.

Main Results:

• Global parameters correlate with resolution, showing tighter clustering at higher resolutions.
• Some structures exhibit clustered distributions even at low resolutions, while others show scatter at high resolutions.
• Local stereochemical parameters reveal specific irregularities, complementing global assessments.

Conclusions:

• Stereochemical parameters provide valuable insights into protein structure reliability.
• These measures offer a simple guide to structure quality, augmenting resolution and R-factor.
• A software suite is under development to automate the detection of unusual stereochemistry in protein structures.