Počet záznamů: 1

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

  1. 1.
    0351148 - UOCHB-X 2011 RIV US eng J - Článek v odborném periodiku
    Vymětal, Jiří - Vondrášek, Jiří
    Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study.
    Journal of Physical Chemistry B. Roč. 114, č. 16 (2010), s. 5632-5642 ISSN 1520-6106
    Grant CEP: GA MŠk LC512
    Výzkumný záměr: CEZ:AV0Z40550506
    Klíčová slova: metadynamics * alanine dipeptide * explicit water models
    Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
    Impakt faktor: 3.603, rok: 2010

    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.
    Trvalý link: http://hdl.handle.net/11104/0006157