6,385 results found
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

    Yasuhiro Matsunaga, Yuji Sugita
    A general machine learning scheme for integrating time-series data from single-molecule experiments and molecular dynamics simulations is proposed and successfully demonstrated for the folding dynamics of the WW domain.
    1. Developmental Biology

    Geometric models for robust encoding of dynamical information into embryonic patterns

    Laurent Jutras-Dubé et al.
    Propagation, speed and shapes of genetic waves of expression during development can be modeled by a simple interplay between two transcriptional modules (dynamic/static), which explains robustness and precision of patterning.
    1. Neuroscience

    Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development

    Mehmet Neset Özel et al.
    Long-term live imaging in intact developing Drosophila brains reveals a role for N-Cadherin-mediated fast filopodial dynamics and growth cone stabilization during neural circuit assembly.
    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

    Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Vytautas Gapsys, Bert L de Groot
    We are writing to comment on the article by El Hage et al., 2018 about molecular dynamics simulations of human hemoglobin.
    1. Structural Biology and Molecular Biophysics

    Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes

    Viviana Monje-Galvan, Gregory A Voth
    Unbiased molecular dynamics simulations reveal the insertion mechanism of the lipidated tail of the matrix domain of HIV-1 Gag into realistic membrane models and show its effect on lipid sorting.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Fusion surface structure, function, and dynamics of gamete fusogen HAP2

    Juan Feng et al.
    Structure, dynamics, and mutation of a gamete fusion protein and comparisons to viral homologues suggest that after trimerization the domain bearing the membrane-inserting fusion loops can pivot with respect to the trimer 3-fold axis.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment

    Xinru Wang et al.
    A novel dynamic charge-charge interaction between B56 and a subset of PP2A-B56 substrates is essential for substrate specificity, dephosphorylation and, for KIF4A, binding condensin I.
    1. Neuroscience

    State-dependent brainstem ensemble dynamics and their interactions with hippocampus across sleep states

    Tomomi Tsunematsu et al.
    Sub-second pontine waves functionally interact with hippocampal population activity in a state-dependent manner across sleep states, while brainstem ensemble dynamics exhibit slow, long-lasting state-predictive activity.
    1. Neuroscience

    Causal evidence for lateral prefrontal cortex dynamics supporting cognitive control

    Derek Evan Nee, Mark D'Esposito
    Non-invasive brain stimulation tests and refines a model of lateral prefrontal cortex neural dynamics supporting cognitive control.

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