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Ligand-induced protein stabilization and enhanced molecular dynamics sampling techniques

In: High Performance Computing in Science and Engineering '21

Author

Listed:
  • Timo Schäfer

    (Johannes Gutenberg University, Department of Physics)

  • Andreas C. Joerger

    (Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry)

  • John Spencer

    (University of Sussex, Department of Chemistry, School of Life Sciences)

  • Friederike Schmid

    (Johannes Gutenberg University, Department of Physics)

  • Giovanni Settanni

    (Johannes Gutenberg University, Department of Physics)

Abstract

Molecular dynamics (MD) simulations provide an increasingly important instrument to study protein-materials interaction phenomena, thanks to both the constant improvement of the available computational resources and the refinement of the modeling methods. Here, we summarize the results obtained along two different research directions within our project. First, we show how MD simulations of several cancer mutants of the DNA-binding domain of the tumor suppressor protein p53 allowed to establish the destabilizing effect of the mutations as well as the stabilizing effects of bound ligands. Second, we report on the development of a new reweighting technique for metadynamics simulations that speeds up convergence and may provide an advantage in the case of simulation of large systems.

Suggested Citation

  • Timo Schäfer & Andreas C. Joerger & John Spencer & Friederike Schmid & Giovanni Settanni, 2023. "Ligand-induced protein stabilization and enhanced molecular dynamics sampling techniques," Springer Books, in: Wolfgang E. Nagel & Dietmar H. Kröner & Michael M. Resch (ed.), High Performance Computing in Science and Engineering '21, pages 3-17, Springer.
    • Handle: RePEc:spr:sprchp:978-3-031-17937-2_1
    DOI: 10.1007/978-3-031-17937-2_1
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