1,105 results found
    1. Structural Biology and Molecular Biophysics

    Automated cryo-EM structure refinement using correlation-driven molecular dynamics

    Maxim Igaev et al.
    Correlation-driven molecular dynamics provides a fully automated and human-bias-free framework for quantitative interpretation of modern cryo-electron microscopy data.
    1. Structural Biology and Molecular Biophysics

    Modelling dynamics in protein crystal structures by ensemble refinement

    B Tom Burnley et al.
    A combination of molecular dynamics simulations and X-ray diffraction data has been used to construct more realistic models of proteins and to provide new insights into their interactions with other proteins and biomolecules.
    1. Structural Biology and Molecular Biophysics

    Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

    Takanori Nakane et al.
    Multi-body refinement in RELION allows high-resolution reconstruction and visualisation of molecular motions in cryo-EM single-particle data sets with continuous forms of structural heterogeneity.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

    Ray Yu-Ruei Wang et al.
    Extensive benchmarking reveals that errors made when manually building models into near-atomic-resolution cryoEM density may automatically be corrected using an improved Rosetta-based structure refinement method.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

    Abhishek Singharoy et al.
    New hybrid structure determination methods leveraging the inherent biophysical properties of a macromolecule through molecular dynamics simulations provide accurate and cost-efficient ways of achieving atomic structures from high resolution cryo-electron density maps.
    1. Immunology and Inflammation

    Antibody escape by polyomavirus capsid mutation facilitates neurovirulence

    Matthew D Lauver et al.
    Cryo EM and a custom subvolume refinement approach applied to mouse polyomavirus revealed the in vivo impact of polyomavirus capsid mutations on antiviral antibody immunoevasion and neurovirulence.
    1. Microbiology and Infectious Disease

    Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post–transfer refinement

    Joshua K Michener et al.
    Adapting bacteria to use an introduced metabolic pathway recapitulates natural mutations and offers a novel bioremediation strategy.
    1. Neuroscience

    Corticostriatal dynamics encode the refinement of specific behavioral variability during skill learning

    Fernando J Santos et al.
    Recordings from the mouse brain as animals learn a lever pressing task reveal how the motor system optimizes skill learning by reducing variability in those aspects of task performance that are essential for achieving a goal.
    1. Structural Biology and Molecular Biophysics

    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2

    Dari Kimanius et al.
    Using GPUs for the costly computations in cryo-EM enables structure determination in mere days on a single workstation.
    1. Neuroscience

    A subset of ipRGCs regulates both maturation of the circadian clock and segregation of retinogeniculate projections in mice

    Kylie S Chew et al.
    A single subpopulation of photoreceptors constitutes a shared node in the neural networks that regulate light-dependent maturation of the circadian clock and light-independent refinement of retinal ganglion cell projections to the brain.

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