Glycoinformatics pp 407-429

Part of the Methods in Molecular Biology book series (MIMB, volume 1273) | Cite as

Molecular Dynamics Simulations of Glycoproteins Using CHARMM

  • Sairam S. Mallajosyula
  • Sunhwan Jo
  • Wonpil Im
  • Alexander D. MacKerellJr.
Protocol

Abstract

Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.

Key words

N-glycosylation O-glycosylation Carbohydrates Empirical force field Molecular dynamics simulations 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Sairam S. Mallajosyula
    • 1
  • Sunhwan Jo
    • 2
  • Wonpil Im
    • 2
  • Alexander D. MacKerellJr.
    • 1
  1. 1.Department of Pharmaceutical SciencesUniversity of Maryland School of PharmacyBaltimoreUSA
  2. 2.Department of Molecular Biosciences and Center for Computational BiologyThe University of KansasLawrenceUSA

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