title: The quality and validation of structures from structural genomics.
abstract: Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein-ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement.
authors.affiliation: Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
authors.forename: Marcin J
authors.initials: MJ
authors.lastname: Domagalski
authors.forename: Heping
authors.initials: H
authors.lastname: Zheng
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Zimmerman
authors.forename: Zbigniew
authors.initials: Z
authors.lastname: Dauter
authors.forename: Alexander
authors.initials: A
authors.lastname: Wlodawer
authors.forename: Wladek
authors.initials: W
authors.lastname: Minor
mesh_terms: D057225:Data Mining; D030562:Databases, Protein; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics / Q000379:methods* / Q000592:standards*; D011786:Quality Control; D015203:Reproducibility of Results
chemical_list: D008024:Ligands; D046911:Macromolecular Substances; D011506:Proteins