MODELING ANTIBODY-CARBOHYDRATE COMPLEXES-PART B

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Carbohydrate docking and threading procedures, established on the JAA-F11 antibody, will be developed to improve throughput using a program to automate several steps including glycan motif identification, removal of false positives from docking results using glycan array or STD NMR data as guidelines, and carbohydrate threading of a virtual glycan array for glycans containing the docked motif. Post-processing methods, like molecular dynamics and MM-PB/GBSA calculations will also be automated to provide a better idea of relative binding if more than one docking structure is identified. These methods will be tested on a blood group A antibody.