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A new methodology for the simulation of flexible protein-ligand interactions

Journal Article


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Abstract


  • A methodology has been developed for the simulation of induced fit between a ligand and its target protein. It utilizes constrained molecular dynamics where atoms determined to be immobile from difference distance matrix studies are fixed. Application of this methodology to HIV-1 reverse transcriptase (RT) as the example target protein has demonstrated its robustness. Short simulation times are sufficient to achieve good refinement of docking poses resulting from exchange of structurally dissimilar inhibitors between crystal structures.

Authors


  •   Garner, James A. (external author)
  •   Deadman, John (external author)
  •   Rhodes, David I. (external author)
  •   Griffith, Renate (external author)
  •   Keller, Paul A.

Publication Date


  • 2007

Citation


  • Garner, J. A., Deadman, J., Rhodes, D. I., Griffith, R. & Keller, P. A. (2007). A new methodology for the simulation of flexible protein-ligand interactions. Journal of Molecular Graphics and Modelling, 26 187-197.

Scopus Eid


  • 2-s2.0-34250866828

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1067&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/66

Number Of Pages


  • 10

Start Page


  • 187

End Page


  • 197

Volume


  • 26

Place Of Publication


  • http://www.elsevier.com/wps/find/journaldescription.cws_home/525012/description#description

Abstract


  • A methodology has been developed for the simulation of induced fit between a ligand and its target protein. It utilizes constrained molecular dynamics where atoms determined to be immobile from difference distance matrix studies are fixed. Application of this methodology to HIV-1 reverse transcriptase (RT) as the example target protein has demonstrated its robustness. Short simulation times are sufficient to achieve good refinement of docking poses resulting from exchange of structurally dissimilar inhibitors between crystal structures.

Authors


  •   Garner, James A. (external author)
  •   Deadman, John (external author)
  •   Rhodes, David I. (external author)
  •   Griffith, Renate (external author)
  •   Keller, Paul A.

Publication Date


  • 2007

Citation


  • Garner, J. A., Deadman, J., Rhodes, D. I., Griffith, R. & Keller, P. A. (2007). A new methodology for the simulation of flexible protein-ligand interactions. Journal of Molecular Graphics and Modelling, 26 187-197.

Scopus Eid


  • 2-s2.0-34250866828

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1067&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/66

Number Of Pages


  • 10

Start Page


  • 187

End Page


  • 197

Volume


  • 26

Place Of Publication


  • http://www.elsevier.com/wps/find/journaldescription.cws_home/525012/description#description