2,043 results found
    1. Structural Biology and Molecular Biophysics

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

    Krystel El Hage et al.
    Simulations of the unliganded human hemoglobin tetramer, which for the first time yield a thermodynamically stable system, cast doubts on the use of standard solvent box sizes for molecular dynamics studies of biological macromolecules.
    1. Structural Biology and Molecular Biophysics

    On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size

    Vytautas Gapsys, Bert L de Groot
    The use of adequate statistics is demonstrated to be an essential prerequisite to derive conclusions on thermodynamics and kinetics from molecular simulations.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Krystel El Hage et al.
    We are writing to respond to the comment by Gapsys and de Groot, 2019 on our article about molecular dynamics simulations of human hemoglobin (El Hage et al., 2018).
    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. Epidemiology and Global Health

    Science Forum: Unit of analysis issues in laboratory-based research

    Nick R Parsons et al.
    A simulation study is used to demonstrate how mistakes in identifying the experimental unit and the unit of analysis can lead to incorrect analyses and inappropriate inferences when reporting research studies.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Gene flow mediates the role of sex chromosome meiotic drive during complex speciation

    Colin D Meiklejohn et al.
    Selfish genetic elements may either promote or prevent the evolution of reproductive barriers, depending on the extent of gene flow between species.
    1. Biochemistry and Chemical Biology

    Coupling between the DEAD-box RNA helicases Ded1p and eIF4A

    Zhaofeng Gao et al.
    Ded1p and eIF4A, two RNA helicases that function in eukaryotic translation initiation, interact physically with each other and with the scaffolding protein eIF4G.
    1. Neuroscience

    Extracting grid cell characteristics from place cell inputs using non-negative principal component analysis

    Yedidyah Dordek et al.
    Computational modeling of the brain’s navigation system reveals that place cells can drive the formation of hexagonal patterns experimentally observed in grid cells activity.
    1. Developmental Biology

    T-box3 is a ciliary protein and regulates stability of the Gli3 transcription factor to control digit number

    Uchenna Emechebe et al.
    The transcription and splicing factor T-box3 is present in primary cilia, regulates multiple aspects of limb development, and interacts with members of the protein complex required for the stability and processing of the Gli3 transcription factor.
    1. Cell Biology

    IFT trains in different stages of assembly queue at the ciliary base for consecutive release into the cilium

    Jenna L Wingfield et al.
    Multimegadalton intraflagellar transport (IFT) trains assemble by sequential recruitment of IFT subcomplexes from the cell body to the ciliary basal bodies and tubulin, the main IFT cargo, is loaded briefly before trains depart.

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