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Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation
Modern carbohydrate simulation models have reached a level of maturity whereby their accuracy is often assumed. However, concerning differences have been reported when comparing the conformational predictions of rhamnose-rich polysaccharides between GLYCAM06 and other widely used carbohydrate force...
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| Format: | Thesis |
| Language: | English |
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Department of Computer Science
2023
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| _version_ | 1867613222094241792 |
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| access_status_str | Open Access |
| author | Lazar, Ryan |
| author2 | Kuttel, Michelle |
| author_browse | Kuttel, Michelle Lazar, Ryan |
| author_facet | Kuttel, Michelle Lazar, Ryan |
| author_sort | Lazar, Ryan |
| collection | Thesis |
| description | Modern carbohydrate simulation models have reached a level of maturity whereby their accuracy is often assumed. However, concerning differences have been reported when comparing the conformational predictions of rhamnose-rich polysaccharides between GLYCAM06 and other widely used carbohydrate force fields. This thesis investigates the scope and origin of these differences. We compare Molecular Dynamics simulations of strategically selected saccharide chains, with both the GLYCAM06 and CHARMM36 carbohydrate force fields. We find significant differences in the conformational predictions of the two force fields. More specifically, collapsed, globular conformations occur in the GLYCAM06 simulations, but are absent in the equivalent CHARMM36 results. The collapsing phenomenon is brought about by a gradual folding process, facilitated by instabilities in the GLYCAM06 a-L-Rha(1®X)-a-L-Rha glycosidic linkage that are stabilised by strong intramolecular interactions. The reduced consideration for repulsive Coulombic forces in GLYCAM06, originating from a collective lack of partial aliphatic hydrogen charges, is likely the principle factor behind these differences. This work suggests critical areas for refinement in GLYCAM06 that will be required for the force field to accurately model rhamnose-rich polysaccharides. The insights gained in this work have the potential to assist in the development of more accurate force fields for modelling carbohydrates. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/37461 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:32:42.829Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Department of Computer Science |
| publisherStr | Department of Computer Science |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/37461 Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation Lazar, Ryan Kuttel, Michelle Ravenscroft, Neil Akher, Farideh Computer Science Modern carbohydrate simulation models have reached a level of maturity whereby their accuracy is often assumed. However, concerning differences have been reported when comparing the conformational predictions of rhamnose-rich polysaccharides between GLYCAM06 and other widely used carbohydrate force fields. This thesis investigates the scope and origin of these differences. We compare Molecular Dynamics simulations of strategically selected saccharide chains, with both the GLYCAM06 and CHARMM36 carbohydrate force fields. We find significant differences in the conformational predictions of the two force fields. More specifically, collapsed, globular conformations occur in the GLYCAM06 simulations, but are absent in the equivalent CHARMM36 results. The collapsing phenomenon is brought about by a gradual folding process, facilitated by instabilities in the GLYCAM06 a-L-Rha(1®X)-a-L-Rha glycosidic linkage that are stabilised by strong intramolecular interactions. The reduced consideration for repulsive Coulombic forces in GLYCAM06, originating from a collective lack of partial aliphatic hydrogen charges, is likely the principle factor behind these differences. This work suggests critical areas for refinement in GLYCAM06 that will be required for the force field to accurately model rhamnose-rich polysaccharides. The insights gained in this work have the potential to assist in the development of more accurate force fields for modelling carbohydrates. 2023-03-16T09:52:43Z 2023-03-16T09:52:43Z 2022 2023-03-16T09:49:12Z Master Thesis Masters MSc http://hdl.handle.net/11427/37461 eng application/pdf Department of Computer Science Faculty of Science |
| spellingShingle | Computer Science Lazar, Ryan Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| thesis_degree_str | Master's |
| title | Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| title_full | Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| title_fullStr | Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| title_full_unstemmed | Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| title_short | Comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| title_sort | comparative evaluation of two carbohydrate force fields for modelling polysaccharide conformation |
| topic | Computer Science |
| url | http://hdl.handle.net/11427/37461 |
| work_keys_str_mv | AT lazarryan comparativeevaluationoftwocarbohydrateforcefieldsformodellingpolysaccharideconformation |