ArticleThe journal of physical chemistry. B2019
Framework for Conducting and Analyzing Crystal Simulations of Nucleic Acids to Aid in Modern Force Field Evaluation.
Article in The journal of physical chemistry. B, 2019. 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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Who cites it
4 citing papers in PubMed.
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Article
- Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology.ACS catalysis · 2019Article
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2 authors.
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Abstract
Crystal simulations provide useful tools, along with solution simulations, to test nucleic acid force fields, but should be interpreted with care owing to the difficulty of establishing the environmental conditions needed to reproduce experimental crystal packing. These challenges underscore the need to construct proper protocols for carrying out crystal simulations and analyzing results to identify the origin of deviations from crystallographic data. Toward this end, we introduce a novel framework for B-factor decomposition into additive intramolecular, rotational, and translational atomic fluctuation components and partitioning of each of these components into individual asymmetric unit and lattice contributions. We apply the framework to a benchmark set of A-DNA, Z-DNA, and B-DNA double helix systems of various chain lengths. Overall, the intramolecular deviations from the crystal were quite small (≤1.0 Å), suggesting high accuracy of the force field, whereas crystal packing was not well reproduced. The present work establishes a framework to conduct and analyze crystal simulations that ultimately take on issues of crystal packing and can provide insight into nucleic acid force fields.
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