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Residue‐centric modeling and design of saccharide and glycoconjugate structures
Author(s) -
Labonte Jason W.,
AdolfBryfogle Jared,
Schief William R.,
Gray Jeffrey J.
Publication year - 2017
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.24679
Subject(s) - glycoconjugate , computer science , glycosidic bond , glycan , glycosylation , chemistry , computational biology , biochemistry , biology , glycoprotein , enzyme
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.