title: Antibody-Carbohydrate Recognition from Docked Ensembles Using the AutoMap Procedure.
abstract: Carbohydrate-protein recognition is vital to many processes in health and disease. In particular, elucidation of the structural basis of carbohydrate binding is important to the development of oligosaccharides and oligosaccharide mimetics as vaccines for infectious diseases and cancer. Computational structural techniques are valuable for the study of carbohydrate-protein recognition due to the challenges associated with experimental determination of carbohydrate-protein complexes. AutoMap is a computer program that we have developed to study protein-ligand recognition. AutoMap determines the interactions taking place in a set of highly ranked poses obtained from molecular docking and processes these to identify the protein residues most likely to be involved in interactions. In this protocol, we describe the use of AutoMap and illustrate its suitability for studying antibody recognition of the Lewis Y tetrasaccharide, which is a potential cancer vaccine antigen.
authors.affiliation: Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
authors.forename: Tamir
authors.initials: T
authors.lastname: Dingjan
authors.forename: Mark
authors.initials: M
authors.lastname: Agostino
authors.forename: Paul A
authors.initials: PA
authors.lastname: Ramsland
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Yuriev
mesh_terms: D000906:Antibodies / Q000737:chemistry* / Q000276:immunology*; D002241:Carbohydrates / Q000737:chemistry* / Q000276:immunology*; D006801:Humans; D007983:Lewis Blood Group Antigens / Q000737:chemistry / Q000276:immunology; D008024:Ligands; D008958:Models, Molecular; D009844:Oligosaccharides / Q000737:chemistry / Q000276:immunology; D011506:Proteins / Q000737:chemistry / Q000276:immunology
chemical_list: D000906:Antibodies; D002241:Carbohydrates; D007983:Lewis Blood Group Antigens; C094162:Lewis Y antigen; D008024:Ligands; D009844:Oligosaccharides; D011506:Proteins