ArticleJournal of chemical theory and computation2024
The Conformation of Glycosidic Linkages According to Various Force Fields: Monte Carlo Modeling of Polysaccharides Based on Extrapolation of Short-Chain Properties.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Deciphering the Structure-Immunomodulatory Function Relationships of Homopolysaccharides.Nutrients · 2026Review
- Iduronate Ring Puckering Effects on Preferred Glycosidic Linkage Conformations in Heparin/Heparan Sulfate and Dermatan Sulfate Disaccharides.Molecules (Basel, Switzerland) · 2026Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Studying Several Properties of Emulgel Based on κ-Carrageenan and Its Incorporation as Shortening Material in Cookies.Food science & nutrition · 2025Article
- Is AMOEBA a Good Force Field for Molecular Dynamics Simulations of Carbohydrates?Journal of chemical information and modeling · 2025Review
- Extending the Martini 3 Coarse-Grained Force Field to Hyaluronic Acid.The journal of physical chemistry. B · 2025Article
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Authors and funding
3 authors.
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Abstract
The conformational features of the glycosidic linkage are the most important variable to consider when studying di-, oligo-, and polysaccharide molecules using molecular dynamics (MD) simulations. The accuracy of the theoretical model describing this degree of freedom influences the quality of the results obtained from MD calculations based on this model. This article focuses on the following two issues related to the conformation of the glycosidic linkage. First, we describe the results of a comparative analysis of the predictions of three carbohydrate-dedicated classical force fields for MD simulations, namely, CHARMM, GLYCAM, and GROMOS, in the context of different parameters of structural and energetic nature related to the conformation of selected types of glycosidic linkages, α(1 → 4), β(1 → 3), and β(1 → 4), connecting glucopyranose units. This analysis revealed several differences, mainly concerning the energy levels of the secondary and tertiary conformers and the linkage flexibility within the dominant
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