Supervised
Molecular Dynamics (SuMD) as a Helpful
Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond
Time Scale
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Abstract
Supervised MD (SuMD) is a computational
method that allows the
exploration of ligand–receptor recognition pathway investigations
in a nanosecond (ns) time scale.
It consists of the incorporation of a tabu-like supervision algorithm
on the ligand–receptor approaching distance into a classic
molecular dynamics (MD) simulation
technique. In addition to speeding up the acquisition of the ligand–receptor
trajectory, this implementation facilitates the characterization
of multiple binding events (such as meta-binding, allosteric, and
orthosteric sites) by taking advantage of the all-atom MD simulations
accuracy of a GPCR–ligand complex embedded into explicit lipid–water
environment