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
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.
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.