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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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/20/7626 |
| _version_ | 1797550895234285568 |
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| author | Victor Stroylov Maria Panova Philip Toukach |
| author_facet | Victor Stroylov Maria Panova Philip Toukach |
| author_sort | Victor Stroylov |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T15:36:54Z |
| format | Article |
| id | doaj.art-d9bb3d38714c48e08262d64c7a164d16 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:36:54Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d9bb3d38714c48e08262d64c7a164d162023-11-20T17:12:29ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012120762610.3390/ijms21207626Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond ConformationsVictor Stroylov0Maria Panova1Philip Toukach2N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, RussiaN.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, RussiaN.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, RussiaSix 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.https://www.mdpi.com/1422-0067/21/20/7626carbohydratedisaccharideglycosidic bond conformationmolecular dynamicsNOE simulationdatabase filling |
| spellingShingle | Victor Stroylov Maria Panova Philip Toukach Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations International Journal of Molecular Sciences carbohydrate disaccharide glycosidic bond conformation molecular dynamics NOE simulation database filling |
| title | Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations |
| title_full | Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations |
| title_fullStr | Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations |
| title_full_unstemmed | Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations |
| title_short | Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations |
| title_sort | comparison of methods for bulk automated simulation of glycosidic bond conformations |
| topic | carbohydrate disaccharide glycosidic bond conformation molecular dynamics NOE simulation database filling |
| url | https://www.mdpi.com/1422-0067/21/20/7626 |
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