Cargando…
doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS
[Image: see text] 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 cell–cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simula...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2017
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662928/ https://www.ncbi.nlm.nih.gov/pubmed/28906114 http://dx.doi.org/10.1021/acs.jcim.7b00237 |
_version_ | 1783274737190830080 |
---|---|
author | Danne, Reinis Poojari, Chetan Martinez-Seara, Hector Rissanen, Sami Lolicato, Fabio Róg, Tomasz Vattulainen, Ilpo |
author_facet | Danne, Reinis Poojari, Chetan Martinez-Seara, Hector Rissanen, Sami Lolicato, Fabio Róg, Tomasz Vattulainen, Ilpo |
author_sort | Danne, Reinis |
collection | PubMed |
description | [Image: see text] 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 cell–cell 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. |
format | Online Article Text |
id | pubmed-5662928 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-56629282017-11-01 doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS Danne, Reinis Poojari, Chetan Martinez-Seara, Hector Rissanen, Sami Lolicato, Fabio Róg, Tomasz Vattulainen, Ilpo J Chem Inf Model [Image: see text] 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 cell–cell 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. American Chemical Society 2017-09-14 2017-10-23 /pmc/articles/PMC5662928/ /pubmed/28906114 http://dx.doi.org/10.1021/acs.jcim.7b00237 Text en Copyright © 2017 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Danne, Reinis Poojari, Chetan Martinez-Seara, Hector Rissanen, Sami Lolicato, Fabio Róg, Tomasz Vattulainen, Ilpo doGlycans–Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS |
title | doGlycans–Tools for Preparing
Carbohydrate Structures for Atomistic Simulations of Glycoproteins,
Glycolipids, and Carbohydrate Polymers for GROMACS |
title_full | doGlycans–Tools for Preparing
Carbohydrate Structures for Atomistic Simulations of Glycoproteins,
Glycolipids, and Carbohydrate Polymers for GROMACS |
title_fullStr | doGlycans–Tools for Preparing
Carbohydrate Structures for Atomistic Simulations of Glycoproteins,
Glycolipids, and Carbohydrate Polymers for GROMACS |
title_full_unstemmed | doGlycans–Tools for Preparing
Carbohydrate Structures for Atomistic Simulations of Glycoproteins,
Glycolipids, and Carbohydrate Polymers for GROMACS |
title_short | doGlycans–Tools for Preparing
Carbohydrate Structures for Atomistic Simulations of Glycoproteins,
Glycolipids, and Carbohydrate Polymers for GROMACS |
title_sort | doglycans–tools for preparing
carbohydrate structures for atomistic simulations of glycoproteins,
glycolipids, and carbohydrate polymers for gromacs |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662928/ https://www.ncbi.nlm.nih.gov/pubmed/28906114 http://dx.doi.org/10.1021/acs.jcim.7b00237 |
work_keys_str_mv | AT dannereinis doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT poojarichetan doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT martinezsearahector doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT rissanensami doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT lolicatofabio doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT rogtomasz doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs AT vattulainenilpo doglycanstoolsforpreparingcarbohydratestructuresforatomisticsimulationsofglycoproteinsglycolipidsandcarbohydratepolymersforgromacs |