Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures
Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been im...
| Main Authors: | , , , , |
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| Format: | Journal Article |
| Published: |
American Chemical Society
2009
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| Online Access: | http://hdl.handle.net/20.500.11937/34925 |
| _version_ | 1848754356082442240 |
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| author | Agostillo, M. Jene, C. Boyle, T. Ramsland, Paul Yuriev, E. |
| author_facet | Agostillo, M. Jene, C. Boyle, T. Ramsland, Paul Yuriev, E. |
| author_sort | Agostillo, M. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been implicated in the development of autoimmune diseases and impact areas such as xenotransplantation and cancer treatment. Understanding the nature of antibody-carbohydrate interactions and the method by which saccharides fit into antibody binding sites is important in understanding the recognition process. In silico techniques offer attractive alternatives to experimental methods (X-ray crystallography and NMR) for the study of antibody-carbohydrate complexes. In particular, molecular docking provides information about protein-ligand interactions in systems that are difficult to study with experimental, techniques. Before molecular docking can be used to investigate antibody-carbohydrate complexes, validation of an appropriate docking method is required. In this study, four popular docking programs, Glide, AutoDock, GOLD, and FlexX, were assessed for their ability to accurately dock carbohydrates to antibodies. Comparison of top ranking poses with crystal structures highlighted the strengths and weaknesses of these programs. Rigid docking, in which the protein conformation remains static, and flexible docking, where both the protein and ligand are treated as flexible, were compared. This study has revealed that generally molecular docking of carbohydrates to antibodies has been performed best by Glide. © 2009 American Chemical Society. |
| first_indexed | 2025-11-14T08:39:06Z |
| format | Journal Article |
| id | curtin-20.500.11937-34925 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T08:39:06Z |
| publishDate | 2009 |
| publisher | American Chemical Society |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-349252017-09-13T15:29:36Z Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures Agostillo, M. Jene, C. Boyle, T. Ramsland, Paul Yuriev, E. Cell surface glycoproteins play vital roles in cellular homeostasis and disease. Antibody recognition of glycosylation on different cells and pathogens is critically important for immune surveillance. Conversely, adverse immune reactions resulting from antibody-carbohydrate interactions have been implicated in the development of autoimmune diseases and impact areas such as xenotransplantation and cancer treatment. Understanding the nature of antibody-carbohydrate interactions and the method by which saccharides fit into antibody binding sites is important in understanding the recognition process. In silico techniques offer attractive alternatives to experimental methods (X-ray crystallography and NMR) for the study of antibody-carbohydrate complexes. In particular, molecular docking provides information about protein-ligand interactions in systems that are difficult to study with experimental, techniques. Before molecular docking can be used to investigate antibody-carbohydrate complexes, validation of an appropriate docking method is required. In this study, four popular docking programs, Glide, AutoDock, GOLD, and FlexX, were assessed for their ability to accurately dock carbohydrates to antibodies. Comparison of top ranking poses with crystal structures highlighted the strengths and weaknesses of these programs. Rigid docking, in which the protein conformation remains static, and flexible docking, where both the protein and ligand are treated as flexible, were compared. This study has revealed that generally molecular docking of carbohydrates to antibodies has been performed best by Glide. © 2009 American Chemical Society. 2009 Journal Article http://hdl.handle.net/20.500.11937/34925 10.1021/ci900388a American Chemical Society restricted |
| spellingShingle | Agostillo, M. Jene, C. Boyle, T. Ramsland, Paul Yuriev, E. Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title | Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title_full | Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title_fullStr | Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title_full_unstemmed | Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title_short | Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures |
| title_sort | molecular docking of carbohydrate ligands to antibodies: structural validation against crystal structures |
| url | http://hdl.handle.net/20.500.11937/34925 |