Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale.
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.
Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy.
Davide
D
Sabbadin
Stefano
S
Moro
D055808:Drug Discovery; D006801:Humans; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D043705:Receptor, Adenosine A2A / Q000737:chemistry* / Q000378:metabolism*; D054852:Small Molecule Libraries / Q000378:metabolism*; D013997:Time Factors
D008024:Ligands; D043705:Receptor, Adenosine A2A; D054852:Small Molecule Libraries