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J Chem Inf Model. 2014 Feb 24;54(2):372-6. doi: 10.1021/ci400766b. Epub 2014 Feb 3.

Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale.

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  • 1Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Universit√† di Padova , via Marzolo 5, 35131 Padova, Italy.

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.

PMID:
24456045
DOI:
10.1021/ci400766b
[PubMed - indexed for MEDLINE]
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