ArticleInternational journal of molecular sciences2020
Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations.
Article in International journal of molecular sciences, 2020. 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.
- Synthesis and immunochemical studies of linear oligoglucosides structurally related to the cyclic β-(1→2)-D-glucan of Brucella.Communications chemistry · 2025Article
- Carbohydrate Structure Database: current state and recent developments.Analytical and bioanalytical chemistry · 2025Review
- Complex Carbohydrates and Glycoconjugates: Structure, Functions and Applications.International journal of molecular sciences · 2021Article
- Stochastic Modelling ofMolecules (Basel, Switzerland) · 2021Article
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Authors and funding
3 authors.
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Abstract
Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling.
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