About: Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://glycob.oxfordjournals.org/content/24/1/70
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 further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. 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 further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. (en)
Title	Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation (en)
skos:prefLabel	Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation (en)
skos:notation	RIV/00216224:14310/14:00073439!RIV15-MSM-14310___
http://linked.open...avai/riv/aktivita	P
http://linked.open...avai/riv/aktivity	P(ED1.1.00/02.0068), P(EE2.3.30.0009), P(GA13-25401S)
http://linked.open...iv/cisloPeriodika	1
http://linked.open...vai/riv/dodaniDat	2015
http://linked.open...aciTvurceVysledku	Koča, Jaroslav Mishra, Sushil Kumar
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	14662
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/14:00073439
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	adaptive biasing force simulations; biasing potential; replica-exchange simulation; conformational sampling; molecular dynamics simulation; saccharides (en)
http://linked.open.../riv/klicoveSlovo	adaptive biasing force simulations biasing potential conformational sampling replica-exchange simulation molecular dynamics simulation saccharides
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[0A5A8CD77F42]
http://linked.open...i/riv/nazevZdroje	Glycobiology
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...vavai/riv/projekt	Study of proteins from pathogens involved in host organism recognition Central european institute of technology Employment of Newly Graduated Doctors of Science for Scientific Excellence
http://linked.open...UplatneniVysledku	2014
http://linked.open...v/svazekPeriodika	24
http://linked.open...iv/tvurceVysledku	Koča, Jaroslav Mishra, Sushil Kumar Kara, Mahmut Zacharias, Martin
http://linked.open...ain/vavai/riv/wos	000330838800008
issn	0959-6658
number of pages	15 (xsd:int)
http://bibframe.org/vocab/doi	10.1093/glycob/cwt093
http://localhost/t...ganizacniJednotka	14310

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