1,515 results found
    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

    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
    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
    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

    Structure of the bacterial ribosome at 2 Å resolution

    Zoe L Watson, Fred R Ward ... Jamie HD Cate
    High-resolution maps and models of the bacterial ribosome provide new chemical insights into protein synthesis, and should enable the development of robust tools for cryo-EM structure modeling and refinement.
    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. Structural Biology and Molecular Biophysics

    Regulation of human mTOR complexes by DEPTOR

    Matthias Wälchli, Karolin Berneiser ... Timm Maier
    Structural and functional analysis reveals the mechanistic basis for mammalian target of rapamycin (mTOR)-dependent roles of DEP domain-containing mTOR interacting protein (DEPTOR) in cancer and metabolic regulation.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery

    Dmitry Shvarev, Jannis Schoppe ... Christian Ungermann
    The structure of the yeast HOPS tethering complex suggests how this large complex may catalyze fusion by tethering Rab-decorated membranes and promoting the assembly of SNAREs.
    1. Structural Biology and Molecular Biophysics

    Model-based local density sharpening of cryo-EM maps

    Arjen J Jakobi, Matthias Wilmanns, Carsten Sachse
    Local sharpening of cryo-electron microscopy maps using atomic models can increase the interpretability of densities in cases of resolution variation and facilitates model building and refinement.
    1. Structural Biology and Molecular Biophysics

    Structure of Escherichia coli respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation

    Piotr Kolata, Rouslan G Efremov
    The dynamic structure of respiratory complex I from mesophilic bacterium is revealed and demonstrates existence of uncoupled conformations in the bacterial complex.

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