title: Molecular dynamics simulations of glycoproteins using CHARMM.
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.
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., HSF II-629, Baltimore, MD, 21201, USA.
authors.forename: Sairam S
authors.initials: SS
authors.lastname: Mallajosyula
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
mesh_terms: D001230:Aspergillus / Q000201:enzymology; D005087:Glucan 1,4-alpha-Glucosidase / Q000737:chemistry; D006023:Glycoproteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D012984:Software; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry
chemical_list: D006023:Glycoproteins; D012997:Solvents; D014867:Water; D005087:Glucan 1,4-alpha-Glucosidase