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Issue 45, 2011
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Studying functional dynamics in bio-molecules using accelerated molecular dynamics

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Abstract

Many biologically important processes such as enzyme catalysis, signal transduction, ligand binding and allosteric regulation occur on the micro- to millisecond time-scale. Despite the sustained and rapid increase in available computational power and the development of efficient simulation algorithms, molecular dynamics (MD) simulations of proteins and bio-machines are generally limited to time-scales of tens to hundreds of nano-seconds. In this perspective article we present a comprehensive review of Accelerated Molecular Dynamics (AMD), an extended biased potential molecular dynamics approach that allows for the efficient study of bio-molecular systems up to time-scales several orders of magnitude greater than those accessible using standard classical MD methods, whilst still maintaining a fully atomistic representation of the system. Compared to many other approaches, AMD affords efficient enhanced conformational space sampling without any a priori understanding of the underlying free energy surface, nor does it require the specific prior definition of a reaction coordinate or a set of collective variables. Successful applications of the AMD method, including the study of slow time-scale functional dynamics in folded proteins and the conformational behavior of natively unstructured proteins are discussed and an outline of the different variants and extensions to the standard AMD approach is presented.

Graphical abstract: Studying functional dynamics in bio-molecules using accelerated molecular dynamics

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Publication details

The article was received on 28 Jun 2011, accepted on 12 Sep 2011 and first published on 21 Oct 2011


Article type: Perspective
DOI: 10.1039/C1CP22100K
Citation: Phys. Chem. Chem. Phys., 2011,13, 20053-20065
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    Studying functional dynamics in bio-molecules using accelerated molecular dynamics

    P. R. L. Markwick and J. A. McCammon, Phys. Chem. Chem. Phys., 2011, 13, 20053
    DOI: 10.1039/C1CP22100K

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