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Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

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posted on 24.02.2014, 00:00 authored by Davide Sabbadin, Stefano Moro
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.