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Steered molecular dynamics simulations of protein-ligand interactions

Abstract

Studies of protein-ligand interactions are helpful to elucidating the mechanisms of ligands, providing clues for rational drug design. The currently developed steered molecular dynamics (SMD) is a complementary approach to experimental techniques in investigating the biochemical processes occurring at microsecond or second time scale, thus SMD may provide dynamical and kinetic processes of ligand-receptor binding and unbinding, which cannot be accessed by the experimental methods. In this article, the methodology of SMD is described, and the applications of SMD simulations for obtaining dynamic insights into protein-ligand interactions are illustrated through two of our own examples. One is associated with the simulations of binding and unbinding processes between huperzine A and acetylcholinesterase, and the other is concerned with the unbinding process of α-APAfrom HIV-1 reverse transcriptase.

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Correspondence to Yechun Xu or Jianhua Shen or Xiaomin Luo or Xu Shen or Kaixian Chen or Hualiang Jiang.

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Xu, Y., Shen, J., Luo, X. et al. Steered molecular dynamics simulations of protein-ligand interactions. Sc. China Ser. B-Chem. 47, 355 (2004). https://doi.org/10.1007/BF02990895

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Keywords

  • molecular dynamics simulation
  • steered molecular dynamics simulation
  • atomic force microscope
  • avidin
  • biotin
  • huperzine A
  • acetylcholinesterase
  • HIV-1 reverse transcriptas
  • non-nucleoside RT inhibitor.