Why are MD simulated protein folding times wrong?

    Research output: Chapter in Book/Published conference outputChapter


    The question of significant deviations of protein folding times simulated using molecular dynamics from experimental values is investigated. It is shown that in the framework of Markov State Model (MSM) describing the conformational dynamics of peptides and proteins, the folding time is very sensitive to the simulation model parameters, such as forcefield and temperature. Using two peptides as examples, we show that the deviations in the folding times can reach an order of magnitude for modest variations of the molecular model. We, therefore, conclude that the folding rate values obtained in molecular dynamics simulations have to be treated with care.
    Original languageEnglish
    Title of host publicationAdvances in Computational Biology
    EditorsHamid R. Arabnia
    Number of pages6
    VolumePart 3
    ISBN (Print)9781441959126
    Publication statusPublished - 6 Oct 2010

    Publication series

    NameAdvances in Experimental Medicine and Biology

    Bibliographical note

    The original publication is available at www.springerlink.com


    • molecular dynamics
    • MSM
    • protein folding
    • simulation models
    • VPAL


    Dive into the research topics of 'Why are MD simulated protein folding times wrong?'. Together they form a unique fingerprint.

    Cite this