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Harvesting Free Energy Landscapes in Biological Systems

  • Darren Wragg
  • Angela Casini
  • Stefano LeoniEmail author
Conference paper
Part of the Lecture Notes in Bioengineering book series (LNBE)

Abstract

A sophisticated mechanistic investigation of biological processes is the starting point for the calculation of accurate free energy figures, which enable comparison with experimental results. Applied to drug discovery, the use of molecular methods can guide the formulation and optimisation of novel drugs, specifically targeting molecular processes as they are learned from simulations. This is illustrated here based on two examples, the study of secondary DNA structures (G4s) as target for small gold-based molecules, and the investigation of the mechanisms of glycerol permeation via the membrane channel aquaglyceroporin-3 (AQP3). Both approaches leverage the enhanced sampling efficiency of accelerated molecular dynamics.

Notes

Acknowledgements

This work has made use of resources of the “Cambridge Service for Data Driven Discovery” (CSD3, http://csd3.cam.ac.uk) system operated by the University of Cambridge Research Computing Service (http://www.hpc.cam.ac.uk) funded by EPSRC Tier-2 capital grant EP/P020259/1. We gratefully acknowledge NVIDIA Corporation for the donation of a Quadro P5000 GPU. We thank ARCCA, Cardiff for additional computational support.

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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.School of ChemistryCardiff UniversityCardiffUK
  2. 2.Department of ChemistryTechnical University of MunichGarchingGermany

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