o HEIRARCHICAL NEIMO for studying large scale motions in proteins

NEIMO algorithm developed for doing long timescale MD simulations for very large proteins systems. This captures catalytically active conformations. Shown below is the enzyme phospho glycerate kinase going from open to closed domain conformation

o Protein Folding

  • NEIMO dynamics has been succesfully applied to folding of an extended polyalanine (Ala)20 to a alfa helix from various starting conformations.

    It has been used to measure the helix propensities of various aminoacids Below is a trajectory with leucine substituted in the middle of polyalanine chain showing a transition through a beta sheet.
    o Large Scale Simulations on the Rhinovirus - 14

    Using MPSim code on the massively parallel computers we are trying to understand the uncoating mechanism of the rhinovirus-14 with and without the WIN drugs.

    Rhinovirus Simulations