Critical Assessment of Current Force Fields. Short Peptide Test Case

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F13%3A00392241" target="_blank" >RIV/61388963:_____/13:00392241 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1021/ct300794a" target="_blank" >http://dx.doi.org/10.1021/ct300794a</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/ct300794a" target="_blank" >10.1021/ct300794a</a>

Result language
angličtina
Original language name
Critical Assessment of Current Force Fields. Short Peptide Test Case
Original language 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 f
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
<a href="/en/project/LH11020" target="_blank" >LH11020: Systematic mapping of the conformational space of short peptides through molecular dynamics simulation - a way to understanding of protein structure formation.</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2013
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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