Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F14%3A00073439" target="_blank" >RIV/00216224:14310/14:00073439 - isvavai.cz</a>

Result on the web

<a href="http://glycob.oxfordjournals.org/content/24/1/70" target="_blank" >http://glycob.oxfordjournals.org/content/24/1/70</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/glycob/cwt093" target="_blank" >10.1093/glycob/cwt093</a>

Result language

angličtina

Original language name

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

Original language description

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and furthervalidated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CE - Biochemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2014

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Glycobiology

ISSN

0959-6658

e-ISSN

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Volume of the periodical

24

Issue of the periodical within the volume

1

Country of publishing house

US - UNITED STATES

Number of pages

15

Pages from-to

70-84

UT code for WoS article

000330838800008

EID of the result in the Scopus database

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