Residue-centric modeling and design of saccharide and glycoconjugate structures

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

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)276-287
Number of pages12
JournalJournal of Computational Chemistry
Volume38
Issue number5
DOIs
StatePublished - Feb 15 2017

Keywords

  • Rosetta
  • carbohydrates
  • computation
  • docking
  • glycoconjugates
  • glycoproteins
  • modeling
  • oligosaccharides
  • structure

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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