ArticleCrystals2021
Refinement of RNA Structures Using Amber Force Fields.
Article in Crystals, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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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.
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Who cites it
4 citing papers in PubMed.
- Structural analysis of uridine modifications in solved RNA structures.NAR genomics and bioinformatics · 2026Article
- Semi-automated modeling of reaction states in time-resolved serial femtosecond crystallography using molecular dynamics sampled conformations.Structural dynamics (Melville, N.Y.) · 2025Article
- When does molecular dynamics improve RNA models? Insights from CASP15 and practical guidelines.Computational and structural biotechnology journal · 2025Article
- Integral equation models for solvent in macromolecular crystals.The Journal of chemical physics · 2022Article
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Authors and funding
2 authors.
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Abstract
Atomic models for nucleic acids derived from X-ray diffraction data at low resolution provide much useful information, but the observed scattering intensities can be fit with models that can differ in structural detail. Tradtional geometric restraints favor models that have bond length and angle terms derived from small molecule crystal structures. Here we explore replacing these restraints with energy gradients derived from force fields, including recently developed integral equation models to account for the effects of water molecules and ions that are not part of the explicit model. We compare conventional and force-field based refinements for 22 RNA crystals, ranging in resolution from 1.1 to 3.6 Å. As expected, it can be important to account for solvent screening of charge-charge interactions, especially in the crowded environment of a nucleic acid crystal. The newly refined models can show improvements in torsion angles and hydrogen-bonding interactions, and can significantly reduce unfavorable atomic clashes, while maintaining or improving agreement with observed scattering intensities.
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Registered trials
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