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Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

ABSTRACT: With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangements of large structures and assemblies, albeit at low resolution. We present an overview of recent progress in the field with examples of successful applications highlighting the utility of such hybrid methods and pointing to emerging future directions guided by advances in experimental characterization of biomolecular systems structure and dynamics.

SUBMITTER: Krieger JM

PROVIDER: S-EPMC7666066 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

Krieger James M JM Doruker Pemra P Scott Ana Ligia AL Perahia David D Bahar Ivet I

Current opinion in structural biology 20200701

With the explosion of normal mode analyses (NMAs) based on elastic network models (ENMs) in the last decade, and the proven precision of MD simulations for visualizing interactions at atomic scale, many hybrid methods have been proposed in recent years. These aim at exploiting the best of both worlds: the atomic precision of MD that often fall short of exploring time and length scales of biological interest, and the capability of ENM-NMA to predict the cooperative and often functional rearrangem ...[more]

PMID: 32622329

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