doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

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Danne , R , Poojari , C , Martinez-Seara , H , Rissanen , S , Lolicato , F , Rog , T & Vattulainen , I 2017 , ' doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS ' , Journal of Chemical Information and Modeling , vol. 57 , no. 10 , pp. 2401-2406 . https://doi.org/10.1021/acs.jcim.7b00237

Title: doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS
Author: Danne, Reinis; Poojari, Chetan; Martinez-Seara, Hector; Rissanen, Sami; Lolicato, Fabio; Rog, Tomasz; Vattulainen, Ilpo
Contributor: University of Helsinki, Department of Physics
University of Helsinki, Department of Physics
University of Helsinki, Department of Physics
Date: 2017-10
Language: eng
Number of pages: 6
Belongs to series: Journal of Chemical Information and Modeling
ISSN: 1549-9596
URI: http://hdl.handle.net/10138/228450
Abstract: Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cellcell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.
Subject: MOLECULAR-DYNAMICS SIMULATIONS
GROMOS FORCE-FIELD
CELLULOSE NANOFIBRILS
N-GLYCOSYLATION
PROTEIN
RECEPTOR
CHARMM
CONFORMATION
CHOLESTEROL
MEMBRANES
1182 Biochemistry, cell and molecular biology
221 Nano-technology
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