title: Residue-centric modeling and design of saccharide and glycoconjugate structures.
abstract: The RosettaCarbohydrate framework is a new tool for modeling a wide variety of saccharide and glycoconjugate structures. This report describes the development of the framework and highlights its applications. The framework integrates with established protocols within the Rosetta modeling and design suite, and it handles the vast complexity and variety of carbohydrate molecules, including branching and sugar modifications. To address challenges of sampling and scoring, RosettaCarbohydrate can sample glycosidic bonds, side-chain conformations, and ring forms, and it utilizes a glycan-specific term within its scoring function. Rosetta can work with standard PDB, GLYCAM, and GlycoWorkbench (.gws) file formats. Saccharide residue-specific chemical information is stored internally, permitting glycoengineering and design. Carbohydrate-specific applications described herein include virtual glycosylation, loop-modeling of carbohydrates, and docking of glyco-ligands to antibodies. Benchmarking data are presented and compared to other studies, demonstrating Rosetta's ability to predict glyco-ligand binding. The framework expands the tools available to glycoscientists and engineers. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland, 21218.
authors.forename: Jason W
authors.identifier: 0000-0002-2912-4985
authors.initials: JW
authors.lastname: Labonte
authors.affiliation: Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, 92037.
authors.forename: Jared
authors.initials: J
authors.lastname: Adolf-Bryfogle
authors.affiliation: Department of Immunology and Microbial Science and IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, 92037.|The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, 02139.
authors.forename: William R
authors.initials: WR
authors.lastname: Schief
authors.affiliation: Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland, 21218.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Gray
mesh_terms: D002236:Carbohydrate Conformation; D002241:Carbohydrates / Q000737:chemistry*; D006001:Glycoconjugates / Q000737:chemistry*; D006031:Glycosylation; D008956:Models, Chemical; D062105:Molecular Docking Simulation; D012984:Software; D009626:Terminology as Topic
chemical_list: D002241:Carbohydrates; D006001:Glycoconjugates
keywords: Rosetta; carbohydrates; computation; docking; glycoconjugates; glycoproteins; modeling; oligosaccharides; structure