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Statements

Subject Item
n2:RIV%2F00216224%3A14310%2F14%3A00073439%21RIV15-MSM-14310___
rdf:type
n15:Vysledek skos:Concept
rdfs:seeAlso
http://glycob.oxfordjournals.org/content/24/1/70
dcterms: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.
dcterms:title
Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation
skos:prefLabel
Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation
skos:notation
RIV/00216224:14310/14:00073439!RIV15-MSM-14310___
n3:aktivita
n17:P
n3:aktivity
P(ED1.1.00/02.0068), P(EE2.3.30.0009), P(GA13-25401S)
n3:cisloPeriodika
1
n3:dodaniDat
n12:2015
n3:domaciTvurceVysledku
n4:4347374 n4:3897672
n3:druhVysledku
n16:J
n3:duvernostUdaju
n13:S
n3:entitaPredkladatele
n20:predkladatel
n3:idSjednocenehoVysledku
14662
n3:idVysledku
RIV/00216224:14310/14:00073439
n3:jazykVysledku
n19:eng
n3:klicovaSlova
adaptive biasing force simulations; biasing potential; replica-exchange simulation; conformational sampling; molecular dynamics simulation; saccharides
n3:klicoveSlovo
n7:saccharides n7:conformational%20sampling n7:adaptive%20biasing%20force%20simulations n7:molecular%20dynamics%20simulation n7:biasing%20potential n7:replica-exchange%20simulation
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[0A5A8CD77F42]
n3:nazevZdroje
Glycobiology
n3:obor
n10:CE
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
4
n3:projekt
n11:GA13-25401S n11:EE2.3.30.0009 n11:ED1.1.00%2F02.0068
n3:rokUplatneniVysledku
n12:2014
n3:svazekPeriodika
24
n3:tvurceVysledku
Zacharias, Martin Mishra, Sushil Kumar Koča, Jaroslav Kara, Mahmut
n3:wos
000330838800008
s:issn
0959-6658
s:numberOfPages
15
n18:doi
10.1093/glycob/cwt093
n5:organizacniJednotka
14310