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

被引：66

作者：

Danne, Reinis ^{[1
]}

Poojari, Chetan ^{[1
,2
]}

Martinez-Seara, Hector ^{[1
,3
]}

Rissanen, Sami ^{[1
]}

Lolicato, Fabio ^{[1
,2
]}

Rog, Tomasz ^{[1
,2
]}

Vattulainen, Ilpo ^{[1
,2
,4
]}

机构：

[1] Tampere Univ Technol, Lab Phys, POB 692, FI-33101 Tampere, Finland

[2] Univ Helsinki, Dept Phys, POB 64, FI-00014 Helsinki, Finland

[3] Acad Sci Czech Republ, Inst Organ Chem & Biochem, Flemingovo Nam 2, CR-16610 Prague 6, Czech Republic

[4] Univ Southern Denmark, MEMPHYS Ctr Biomembrane Phys, DK-5230 Odense, Denmark

来源：

JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2017年 / 57卷 / 10期

基金：

芬兰科学院; 欧洲研究理事会;

关键词：

FORCE-FIELD; CELLULOSE NANOFIBRILS; N-GLYCOSYLATION; PROTEIN; RECEPTOR; CONFORMATION; CHOLESTEROL;

D O I：

10.1021/acs.jcim.7b00237

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

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.

引用

页码：2401 / 2406

页数：6

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