Simplified quality assessment for small-molecule ligands in the Protein Data Bank.

By Chenghua Shao, John D. Westbrook, Changpeng Lu, Charmi Bhikadiya, E. Peisach, Jasmine Y. Young, Jose M. Duarte, Robert Lowe, Sijian Wang, Yana Rose and 2 more. 2022

20 citations recorded by the source corpus.

SUMMARY More than 70% of the experimentally determined macromolecular structures in the Protein Data Bank (PDB) contain small-molecule ligands. Quality indicators of ~643,000 ligands present in ~106,000 PDB X-ray crystal structures have been analyzed. Ligand quality varies greatly with regard to goodness-of-fit between ligand structure and experimental data, deviations in bond lengths and angles from known chemical structures, and inappropriate interatomic clashes between the ligand and its surroundings. Based on Principal Component Analysis, correlated quality indicators of ligand structure have been aggregated into two largely orthogonal composite indicators measuring goodness-of-fit to experimental data and deviation from ideal chemical structure. Ranking of the composite quality indicators across the PDB archive enabled construction of uniformly distributed composite ranking score. This score is implemented at RCSB.org to compare chemically identical ligands in distinct PDB structures with easy-to-interpret 2D ligand quality plots, allowing PDB users to quickly assess ligand structure quality and select best exemplars.

Subfields: Cell Biology, Materials Chemistry, Molecular Biology