Details

Autor(en) / Beteiligte

• Labonte, Jason W.
• Adolf‐Bryfogle, Jared
• Schief, William R.
• Gray, Jeffrey J.

Titel

Residue‐centric modeling and design of saccharide and glycoconjugate structures

Ist Teil von

• Journal of computational chemistry, 2017-02, Vol.38 (5), p.276-287

Ort / Verlag

United States: Wiley Subscription Services, Inc

Erscheinungsjahr

2017

Link zum Volltext

Quelle

Wiley Online Library Journals Frontfile Complete

Beschreibungen/Notizen

• 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. Carbohydrates are present everywhere in nature, possessing a vast array of structural diversity, yet historically, they have been challenging to model. RosettaCarbohydrate is a new tool for researchers studying the form and function of carbohydrate structures. The framework integrates with Rosetta's successful modeling and design suite and addresses challenges unique to glycans. This article describes the development of the framework and highlights its applications, including loop modeling and glyco‐ligand docking.