Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study

Kód výsledku v 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>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study

Popis výsledku anglicky

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.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CF - Fyzikální chemie a teoretická chemie

OECD FORD obor

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Projekt

<a href="/cs/project/LC512" target="_blank" >LC512: Centrum biomolekul a komplexních molekulových systémů</a><br>

Návaznosti

Z - Vyzkumny zamer (s odkazem do CEZ)

Rok uplatnění

2010

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

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Svazek periodika

114

Číslo periodika v rámci svazku

16

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

11

Strana od-do

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Kód UT WoS článku

000276889100050

EID výsledku v databázi Scopus

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