This HTML5 document contains 44 embedded RDF statements represented using HTML+Microdata notation.

The embedded RDF content will be recognized by any processor of HTML5 Microdata.

Namespace Prefixes

PrefixIRI
dctermshttp://purl.org/dc/terms/
n17http://linked.opendata.cz/resource/domain/vavai/projekt/
n5http://linked.opendata.cz/resource/domain/vavai/riv/tvurce/
n19http://linked.opendata.cz/resource/domain/vavai/subjekt/
n13http://linked.opendata.cz/ontology/domain/vavai/
shttp://schema.org/
skoshttp://www.w3.org/2004/02/skos/core#
n4http://linked.opendata.cz/ontology/domain/vavai/riv/
n3http://bibframe.org/vocab/
n2http://linked.opendata.cz/resource/domain/vavai/vysledek/
rdfhttp://www.w3.org/1999/02/22-rdf-syntax-ns#
n18http://linked.opendata.cz/resource/domain/vavai/vysledek/RIV%2F61388963%3A_____%2F13%3A00392241%21RIV14-MSM-61388963/
n12http://linked.opendata.cz/ontology/domain/vavai/riv/klicoveSlovo/
n8http://linked.opendata.cz/ontology/domain/vavai/riv/duvernostUdaju/
xsdhhttp://www.w3.org/2001/XMLSchema#
n16http://linked.opendata.cz/ontology/domain/vavai/riv/jazykVysledku/
n10http://linked.opendata.cz/ontology/domain/vavai/riv/aktivita/
n15http://linked.opendata.cz/ontology/domain/vavai/riv/obor/
n14http://linked.opendata.cz/ontology/domain/vavai/riv/druhVysledku/
n7http://reference.data.gov.uk/id/gregorian-year/

Statements

Subject Item
n2:RIV%2F61388963%3A_____%2F13%3A00392241%21RIV14-MSM-61388963
rdf:type
n13:Vysledek skos:Concept
dcterms:description
The applicability of molecular dynamics simulations for studies of protein folding or intrinsically disordered proteins critically depends on quality of energetic functions-force fields. The four popular force fields for biomolecular simulations, CHARMM22/CMAP, AMBER FF03, AMBER FF99SB, and OPLS-AA/L, were compared in prediction of conformational propensities of all common proteinogenic amino acids. The minimalistic model of terminally block amino acids (dipeptides) was chosen for assessment of side chain effects on backbone propensities. The precise metadynamics simulations revealed striking inconsistency of trends in conformational preferences as manifested by investigated force fields for both backbone and side chains. To trace this disapproval between force fields, the two related AMBER force fields were studied more closely. In the cases of FF99SB and FF03, we uncovered that the distinct tends were driven by different charge models. Additionally, the effects of recent correction for side chain torsion (FF99SB-LLDN) were examined on affected amino acids and exposed significant coupling between free energy profiles and propensities of backbone and side chain conformers. These findings have important consequences for further force field development. The applicability of molecular dynamics simulations for studies of protein folding or intrinsically disordered proteins critically depends on quality of energetic functions-force fields. The four popular force fields for biomolecular simulations, CHARMM22/CMAP, AMBER FF03, AMBER FF99SB, and OPLS-AA/L, were compared in prediction of conformational propensities of all common proteinogenic amino acids. The minimalistic model of terminally block amino acids (dipeptides) was chosen for assessment of side chain effects on backbone propensities. The precise metadynamics simulations revealed striking inconsistency of trends in conformational preferences as manifested by investigated force fields for both backbone and side chains. To trace this disapproval between force fields, the two related AMBER force fields were studied more closely. In the cases of FF99SB and FF03, we uncovered that the distinct tends were driven by different charge models. Additionally, the effects of recent correction for side chain torsion (FF99SB-LLDN) were examined on affected amino acids and exposed significant coupling between free energy profiles and propensities of backbone and side chain conformers. These findings have important consequences for further force field development.
dcterms:title
Critical Assessment of Current Force Fields. Short Peptide Test Case Critical Assessment of Current Force Fields. Short Peptide Test Case
skos:prefLabel
Critical Assessment of Current Force Fields. Short Peptide Test Case Critical Assessment of Current Force Fields. Short Peptide Test Case
skos:notation
RIV/61388963:_____/13:00392241!RIV14-MSM-61388963
n13:predkladatel
n19:ico%3A61388963
n4:aktivita
n10:I n10:P
n4:aktivity
I, P(LH11020)
n4:cisloPeriodika
1
n4:dodaniDat
n7:2014
n4:domaciTvurceVysledku
n5:1136933 n5:7358946
n4:druhVysledku
n14:J
n4:duvernostUdaju
n8:S
n4:entitaPredkladatele
n18:predkladatel
n4:idSjednocenehoVysledku
67310
n4:idVysledku
RIV/61388963:_____/13:00392241
n4:jazykVysledku
n16:eng
n4:klicovaSlova
Helix-coil transition; protein-folding simulations; amino-acids; side-chain; alanine dipeptide
n4:klicoveSlovo
n12:Helix-coil%20transition n12:side-chain n12:amino-acids n12:protein-folding%20simulations n12:alanine%20dipeptide
n4:kodStatuVydavatele
US - Spojené státy americké
n4:kontrolniKodProRIV
[B7DE7E3D39A1]
n4:nazevZdroje
Journal of Chemical Theory and Computation
n4:obor
n15:CF
n4:pocetDomacichTvurcuVysledku
2
n4:pocetTvurcuVysledku
2
n4:projekt
n17:LH11020
n4:rokUplatneniVysledku
n7:2013
n4:svazekPeriodika
9
n4:tvurceVysledku
Vondrášek, Jiří Vymětal, Jiří
n4:wos
000313378700047
s:issn
1549-9618
s:numberOfPages
11
n3:doi
10.1021/ct300794a