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Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F10%3A00351148%21RIV11-MSM-61388963
rdf:type
skos:Concept n17:Vysledek
dcterms:description
We have utilized metadynamics for the conformational study of the solvated alanine dipeptide molecule, and our results show that the method has proven to be competent as a fast, robust, and reliable method for the conformation free-energy calculations of peptides in an explicit solvent, surpassing traditional methods such as umbrella sampling. We have also addressed the issue of the influence of different water models on the resulting free-energy profile in order to consistently decompose the setting of our simulation. All of the explicit water models for the simulation of biomolecules TIP3P, TIP4P, TIP4P/Ew, TIP5P, and SPCE have exhibited similar effects on the conformational preferences of alanine dipeptide with no significant differences. All of the tested force fields (ff03, ff99SB, opls-aa, and charmm27) appreciably differ in the population of the individual conformers and the barriers between them. We have utilized metadynamics for the conformational study of the solvated alanine dipeptide molecule, and our results show that the method has proven to be competent as a fast, robust, and reliable method for the conformation free-energy calculations of peptides in an explicit solvent, surpassing traditional methods such as umbrella sampling. We have also addressed the issue of the influence of different water models on the resulting free-energy profile in order to consistently decompose the setting of our simulation. All of the explicit water models for the simulation of biomolecules TIP3P, TIP4P, TIP4P/Ew, TIP5P, and SPCE have exhibited similar effects on the conformational preferences of alanine dipeptide with no significant differences. All of the tested force fields (ff03, ff99SB, opls-aa, and charmm27) appreciably differ in the population of the individual conformers and the barriers between them.
dcterms:title
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
skos:prefLabel
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
skos:notation
RIV/61388963:_____/10:00351148!RIV11-MSM-61388963
n3:aktivita
n14:Z n14:P
n3:aktivity
P(LC512), Z(AV0Z40550506)
n3:cisloPeriodika
16
n3:dodaniDat
n7:2011
n3:domaciTvurceVysledku
n11:1136933 n11:7358946
n3:druhVysledku
n15:J
n3:duvernostUdaju
n10:S
n3:entitaPredkladatele
n12:predkladatel
n3:idSjednocenehoVysledku
270585
n3:idVysledku
RIV/61388963:_____/10:00351148
n3:jazykVysledku
n18:eng
n3:klicovaSlova
metadynamics; alanine dipeptide; explicit water models
n3:klicoveSlovo
n4:alanine%20dipeptide n4:metadynamics n4:explicit%20water%20models
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[5E7AC4405548]
n3:nazevZdroje
Journal of Physical Chemistry B
n3:obor
n8:CF
n3:pocetDomacichTvurcuVysledku
2
n3:pocetTvurcuVysledku
2
n3:projekt
n13:LC512
n3:rokUplatneniVysledku
n7:2010
n3:svazekPeriodika
114
n3:tvurceVysledku
Vymětal, Jiří Vondrášek, Jiří
n3:wos
000276889100050
n3:zamer
n9:AV0Z40550506
s:issn
1520-6106
s:numberOfPages
11