ArticleMethods in molecular biology (Clifton, N.J.)2014
The quality and validation of structures from structural genomics.
Article in Methods in molecular biology (Clifton, N.J.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- PinMyMetal: a hybrid learning system to accurately model transition metal binding sites in macromolecules.Nature communications · 2025Article
- DIPS-Plus: The enhanced database of interacting protein structures for interface prediction.Scientific data · 2023Article
- RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.NAR genomics and bioinformatics · 2023Article
- Using machine learning to predict the effects and consequences of mutations in proteins.Current opinion in structural biology · 2023Review
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
- CMM-An enhanced platform for interactive validation of metal binding sites.Protein science : a publication of the Protein Society · 2023Article
- 'International journal of molecular sciences · 2021Article
- On the evolution of the quality of macromolecular models in the PDB.The FEBS journal · 2020Article
- Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.Journal of chemical theory and computation · 2020Article
- How accurate are accurate force-fields for B-DNA?Nucleic acids research · 2017Article
- A public database of macromolecular diffraction experiments.Acta crystallographica. Section D, Structural biology · 2016Article
- Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Review
- Single nucleotide variations: biological impact and theoretical interpretation.Protein science : a publication of the Protein Society · 2014Review
- Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.IUCrJ · 2014Article
- The future of crystallography in drug discovery.Expert opinion on drug discovery · 2014Review
Corrections and comments
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Authors and funding
6 authors.
Funding
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.
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