Curtin University Homepage
  • Library
  • Help
    • Admin

    espace - Curtin’s institutional repository

    JavaScript is disabled for your browser. Some features of this site may not work without it.
    View Item 
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item
    • espace Home
    • espace
    • Curtin Research Publications
    • View Item

    A bias-exchange approach to protein folding

    20314_downloaded_stream_302.pdf (321.7Kb)
    20313_downloaded_stream_301.pdf (821.6Kb)
    Access Status
    Open access
    Authors
    Piana, Stefano
    Laio, A.
    Date
    2007
    Type
    Journal Article
    
    Metadata
    Show full item record
    Citation
    Piana, Stefano and Laio, Alessandro. 2007. A bias-exchange approach to protein folding. Journal of Physical Chemistry B 111 (17): 4553-4559.
    Source Title
    Journal of Physical Chemistry B
    Additional URLs
    http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2007/111/i17/pdf/jp067873l.pdf
    Faculty
    Department of Applied Chemistry
    Division of Engineering, Science and Computing
    Faculty of Science
    Funding and Sponsorship
    http://purl.org/au-research/grants/arc/DP0558938
    Remarks

    The website for the Journal of Physical Chemistry B is available at: http://pubs.acs.org/journals/jpcbfk/index.html

    URI
    http://hdl.handle.net/20.500.11937/15651
    Collection
    • Curtin Research Publications
    Abstract

    By suitably extending a recent approach [G. Bussi et al, J Am Chem Soc 2006, 128, 13435] we introduce a powerful methodology that allows the parallel reconstruction of the free energy of a system in a virtually unlimited number of variables. Multiple metadynamics simulations of the same system at the same temperature are performed, biasing each replica with a time-dependent potential constructed in a different set of collective variables. Exchanges between the bias potentials in the different variables are periodically allowed according to a replica exchange scheme. Due to the efficaciously multidimensional nature of the bias the method allows exploring complex free energy landscapes with high efficiency. The usefulness of the method is demonstrated by performing an atomistic simulation in explicit solvent of the folding of a Triptophane cage miniprotein. It is shown that the folding free energy landscape can be fully characterized starting from an extended conformation using only 40 ns of simulation on 8 replicas.

    Related items

    Showing items related by title, author, creator and subject.

    • Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods to Reproduce the Behavior of Fluorescent Labels on Proteins
      Walczewska-Szewc, K.; Deplazes, Evelyne; Corry, B. (2015)
      Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for ...
    • Grand Canonical Monte Carlo Simulation Study of Hydrogen Storage in Ordered Mesoporous Carbons at 303 K
      Kowalczyk, Poitr; Jaroniec, M.; Solarz, L.; Terzyk, A.; Gauden, P. (2006)
      ABSTRACT: Results of Grand Canonical Monte Carlo (GCMC) simulations of hydrogen storage at 303 K in ordered mesoporous carbons (OMCs) which are inverse replicas of cubic Im3 — m silica are presented. Of the ones ...
    • Computational Insights into Mg2+ Dehydration in the Presence of Carbonate
      Aufort, Julie ; Raiteri, Paolo ; Gale, Julian (2022)
      Water exchange around a free magnesium ion and magnesium paired with carbonate in aqueous solution was studied using free energy methods. Both a rigid-ion and a polarizable force field based on the AMOEBA model were ...
    Advanced search

    Browse

    Communities & CollectionsIssue DateAuthorTitleSubjectDocument TypeThis CollectionIssue DateAuthorTitleSubjectDocument Type

    My Account

    Admin

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Follow Curtin

    • 
    • 
    • 
    • 
    • 

    CRICOS Provider Code: 00301JABN: 99 143 842 569TEQSA: PRV12158

    Copyright | Disclaimer | Privacy statement | Accessibility

    Curtin would like to pay respect to the Aboriginal and Torres Strait Islander members of our community by acknowledging the traditional owners of the land on which the Perth campus is located, the Whadjuk people of the Nyungar Nation; and on our Kalgoorlie campus, the Wongutha people of the North-Eastern Goldfields.