Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations

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 p...

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Bibliographic Details
Published inInternational journal of molecular sciences Vol. 21; no. 20; p. 7626
Main Authors Stroylov, Victor, Panova, Maria, Toukach, Philip
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 15.10.2020
MDPI
Subjects
Accuracy
Automation
carbohydrate
Carbohydrate Conformation
Carbohydrate Sequence
Carbohydrates
Conformation
database filling
Density functional theory
disaccharide
Disaccharides
Disaccharides - chemistry
glycosidic bond conformation
Methods
Molecular dynamics
Molecular Dynamics Simulation - standards
NOE simulation
Simulation
Software
Software - standards
Solvents
Solvents - chemistry
force field
database filling
NOE simulation
nuclear Overhauser effect
disaccharide
molecular dynamics
glycosidic bond conformation
carbohydrate
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Summary: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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ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms21207626