Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F10%3A00351148" target="_blank" >RIV/61388963:_____/10:00351148 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Alternative languages
Result language
angličtina
Original language name
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
Original language 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 ofpeptides 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 ofour 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 thetested force fields (ff03, ff99SB, opls-aa, and charmm27) appreciably differ in the population of the individual conformers and the barriers between them.
Czech name
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Czech description
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Classification
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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Result continuities
Project
<a href="/en/project/LC512" target="_blank" >LC512: Center for biomolecules and complex molecular systems</a><br>
Continuities
Z - Vyzkumny zamer (s odkazem do CEZ)
Others
Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
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Volume of the periodical
114
Issue of the periodical within the volume
16
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
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UT code for WoS article
000276889100050
EID of the result in the Scopus database
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