ArticleActa crystallographica Section B, Structural science, crystal engineering and materials2019
Accurate geometrical restraints for Watson-Crick base pairs.
Article in Acta crystallographica Section B, Structural science, crystal engineering and materials, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.Acta crystallographica. Section D, Structural biology · 2026Article
- Cat_Wiz: a stereochemistry-guided toolkit for locating, diagnosing, and annotating Mg2+ ions in RNA structures.Nucleic acids research · 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
- In situ ligand restraints from quantum-mechanical methods.Acta crystallographica. Section D, Structural biology · 2023Article
- Mechanism of RNA polymerase I selection by transcription factor UAF.Science advances · 2022Article
- 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
- Conformation-dependent restraints for polynucleotides: the sugar moiety.Nucleic acids research · 2020Article
- New insights and innovation from a million crystal structures in the Cambridge Structural Database.Structural dynamics (Melville, N.Y.) · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Geometrical restraints provide key structural information for the determination of biomolecular structures at lower resolution by experimental methods such as crystallography or cryo-electron microscopy. In this work, restraint targets for nucleic acids bases are derived from three different sources and compared: small-molecule crystal structures in the Cambridge Structural Database (CSD), ultrahigh-resolution structures in the Protein Data Bank (PDB) and quantum-mechanical (QM) calculations. The best parameters are those based on CSD structures. After over two decades, the standard library of Parkinson et al. [(1996), Acta Cryst. D52, 57-64] is still valid, but improvements are possible with the use of the current CSD database. The CSD-derived geometry is fully compatible with Watson-Crick base pairs, as comparisons with QM results for isolated and paired bases clearly show that the CSD targets closely correspond to proper base pairing. While the QM results are capable of distinguishing between single and paired bases, their level of accuracy is, on average, nearly two times lower than for the CSD-derived targets when gauged by root-mean-square deviations from ultrahigh-resolution structures in the PDB. Nevertheless, the accuracy of QM results appears sufficient to provide stereochemical targets for synthetic base pairs where no reliable experimental structural information is available. To enable future tests for this approach, QM calculations are provided for isocytosine, isoguanine and the iCiG base pair.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.