ArticleActa crystallographica. Section D, Biological crystallography2014
Automated identification of elemental ions in macromolecular crystal structures.
Article in Acta crystallographica. Section D, Biological crystallography, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
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- Observation of the Assembly of the Nascent Mineral Core at the Nucleation Site of Human Mitochondrial Ferritin.Journal of the American Chemical Society · 2025Article
- Utilizing anomalous signals for element identification in macromolecular crystallography.Acta crystallographica. Section D, Structural biology · 2024Article
- A database overview of metal-coordination distances in metalloproteins.Acta crystallographica. Section D, Structural biology · 2024Article
- Exploiting the full potential of cryo-EM maps.BBA advances · 2024Article
- Experimental detection of conformational transitions between forms of DNA: problems and prospects.Biophysical reviews · 2023Review
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- Article
- Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones.ACS chemical biology · 2022Article
- Divergent evolution of extreme production of variant plant monounsaturated fatty acids.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structures of nonsense-mediated mRNA decay factors UPF3B and UPF3A in complex with UPF2 reveal molecular basis for competitive binding and for neurodevelopmental disorder-causing mutation.Nucleic acids research · 2022Article
- The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (MbioRxiv : the preprint server for biology · 2021Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Illuminating the allosteric modulation of the calcium-sensing receptor.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.Protein science : a publication of the Protein Society · 2020Article
- Finding High-Quality Metal Ion-Centric Regions Across the Worldwide Protein Data Bank.Molecules (Basel, Switzerland) · 2019Article
- Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data.Acta crystallographica. Section D, Structural biology · 2019Article
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9 authors.
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Abstract
Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed.
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