Počet záznamů: 1

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

SYSNO ASEP	0351148
Druh ASEP	J - Článek v odborném periodiku
Zařazení RIV	J - Článek v odborném periodiku
Poddruh J	Článek ve WOS
Název	Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
Tvůrce(i)	Vymětal, Jiří (UOCHB-X)_{RID, ORCID} Vondrášek, Jiří (UOCHB-X)_{RID, ORCID}
Celkový počet autorů	2
Zdroj.dok.	Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106 Roč. 114, č. 16 (2010), s. 5632-5642
Poč.str.	11 s.
Jazyk dok.	eng - angličtina
Země vyd.	US - Spojené státy americké
Klíč. slova	metadynamics ; alanine dipeptide ; explicit water models
Vědní obor RIV	CF - Fyzikální chemie a teoretická chemie
CEP	LC512 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy
CEZ	AV0Z40550506 - UOCHB-X (2005-2011)
UT WOS	000276889100050
DOI	10.1021/jp100950w
Anotace	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.
Pracoviště	Ústav organické chemie a biochemie
Kontakt	asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434
Rok sběru	2011

Počet záznamů: 1