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

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

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.

Publication types

  • Letter
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Drug Discovery
  • Humans
  • Ligands
  • Molecular Dynamics Simulation*
  • Protein Binding
  • Protein Conformation
  • Receptor, Adenosine A2A / chemistry*
  • Receptor, Adenosine A2A / metabolism*
  • Small Molecule Libraries / metabolism*
  • Time Factors

Substances

  • Ligands
  • Receptor, Adenosine A2A
  • Small Molecule Libraries