The quality and validation of structures from structural genomics

Marcin J. Domagalski, Heping Zheng, Matthew D. Zimmerman, Zbigniew Dauter, Alexander Wlodawer, Wladek Minor

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

24 Scopus citations

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.

Original languageEnglish
Title of host publicationStructural Genomics
Subtitle of host publicationGeneral Applications
PublisherHumana Press Inc.
Pages297-314
Number of pages18
ISBN (Print)9781627036900
DOIs
StatePublished - 2014
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1091
ISSN (Print)1064-3745

Keywords

  • Data mining
  • Drug discovery
  • Structural genomics
  • Structure quality
  • Structure validation

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