ArticleJournal of computer-aided molecular design2022
Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives.
Article in Journal of computer-aided molecular design, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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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3 citing papers in PubMed, 8 citations in OpenAlex.
- Destabilization of Structured RNAs by OPC and TIP4PD Water Models.Journal of chemical theory and computation · 2026Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes.RNA (New York, N.Y.) · 2024Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
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Abstract
Pseudouridine is one of the most abundant post-transcriptional modifications in RNA. We have previously shown that the FF99-derived parameters for pseudouridine and some of its naturally occurring derivatives in the AMBER distribution either alone or in combination with the revised γ torsion parameters (parmbsc0) failed to reproduce their conformational characteristics observed experimentally (Deb et al. in J Chem Inf Model 54:1129-1142, 2014; Deb et al. in J Comput Chem 37:1576-1588, 2016; Dutta et al. in J Chem Inf Model 60:4995-5002, 2020). However, the application of the recommended bsc0 correction did lead to an improvement in the description not only of the distribution in the γ torsional space but also of the sugar pucker distributions. In an earlier study, we examined the transferability of the revised glycosidic torsion parameters (χ
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