ArticleNucleic acids research2016
Conformation-dependent restraints for polynucleotides: I. Clustering of the geometry of the phosphodiester group.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.Acta crystallographica. Section D, Structural biology · 2026Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- Validated ligand geometries for macromolecular refinement restraints and molecular mechanics force fields.bioRxiv : the preprint server for biology · 2025Article
- When will RNA get its AlphaFold moment?Nucleic acids research · 2023Article
- Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method.Acta crystallographica. Section D, Structural biology · 2023Article
- New restraints and validation approaches for nucleic acid structures in PDB-REDO.Acta crystallographica. Section D, Structural biology · 2021Article
- Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2021Article
- Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.Protein science : a publication of the Protein Society · 2021Article
- On the evolution of the quality of macromolecular models in the PDB.The FEBS journal · 2020Article
- Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples.Nucleic acids research · 2020Article
- Conformation-dependent restraints for polynucleotides: the sugar moiety.Nucleic acids research · 2020Article
- Accurate geometrical restraints for Watson-Crick base pairs.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2019Article
- The crystal structure of Z-DNA with untypically coordinated CaJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2018Article
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3 authors.
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Abstract
The refinement of macromolecular structures is usually aided by prior stereochemical knowledge in the form of geometrical restraints. Such restraints are also used for the flexible sugar-phosphate backbones of nucleic acids. However, recent highly accurate structural studies of DNA suggest that the phosphate bond angles may have inadequate description in the existing stereochemical dictionaries. In this paper, we analyze the bonding deformations of the phosphodiester groups in the Cambridge Structural Database, cluster the studied fragments into six conformation-related categories and propose a revised set of restraints for the O-P-O bond angles and distances. The proposed restraints have been positively validated against data from the Nucleic Acid Database and an ultrahigh-resolution Z-DNA structure in the Protein Data Bank. Additionally, the manual classification of PO4 geometry is compared with geometrical clusters automatically discovered by machine learning methods. The machine learning cluster analysis provides useful insights and a practical example for general applications of clustering algorithms for automatic discovery of hidden patterns of molecular geometry. Finally, we describe the implementation and application of a public-domain web server for automatic generation of the proposed restraints.
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