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. Crystallographic structures of protein-ligand complexes are ideal for understanding the mechanism of recognition, however, crystallizing protein-ligand complexes is often more difficult than crystallization of the protein alone. Several other experimental methods (mutation studies, NMR STDs, and glycan arrays) provide insight into the orientation, specificity and binding pocket contacts that can be used to aid in computational prediction methods. This project uses glycan array data to assist in predicting the complex of the JAA-F11 antibody with the TF-antigen through use of a new, high-throughput technique called Carbohydrate Threading. This technique allows quantitative comparisons of different glycans modeled onto a template structure, like a docked model, to determine the capacity of a binding pocket to spatially accommodate a known binder or non-binder.
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