1,755 results found
    1. Structural Biology and Molecular Biophysics

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

    Maxim Igaev, Carsten Kutzner ... Helmut Grubmüller
    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, Pavel V Afonine ... Piet Gros
    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, Dari Kimanius ... Sjors HW Scheres
    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. Developmental Biology

    The Cl--channel TMEM16A is involved in the generation of cochlear Ca2+ waves and promotes the refinement of auditory brainstem networks in mice

    Alena Maul, Antje Kathrin Huebner ... Christian A Hübner
    Ano1 deletion disrupts Ca2+ waves within Kölliker’s organ, reduces burst-firing activity and frequency selectivity of auditory brainstem neurons in the medial nucleus of the trapezoid body, and impairs the functional refinement of its projections to the lateral superior olive.
    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, Ivan Teo ... Klaus Schulten
    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. 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, Yifan Song ... Frank DiMaio
    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

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

    Dari Kimanius, Björn O Forsberg ... Erik Lindahl
    Using GPUs for the costly computations in cryo-EM enables structure determination in mere days on a single workstation.
    1. Microbiology and Infectious Disease

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

    Joshua K Michener, Aline A Camargo Neves ... Christopher J Marx
    Adapting bacteria to use an introduced metabolic pathway recapitulates natural mutations and offers a novel bioremediation strategy.
    1. Developmental Biology

    Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis

    Jeff Jiajing Zhou, Jin Sun Cho ... Ken WY Cho
    Histone deacetylase 1 (Hdac1) plays a crucial role in maintaining differential histone acetylation states of enhancers in various germ layers and regulates the transcriptional program both temporally and spatially.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Genetic variation in ALDH4A1 is associated with muscle health over the lifespan and across species

    Osvaldo Villa, Nicole L Stuhr ... Sean P Curran
    Leveraging the US Health and Retirement Study and C. elegans genetics reveals ALDH4A1/alh-6 as an evolutionarily conserved biomarker for normal muscle function over the lifespan.
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