Calculation of free energy changes due to mutations from alchemical free energy simulations

  title={Calculation of free energy changes due to mutations from alchemical free energy simulations},
  author={Muhammad Harunur Rashid and Germano Heinzelmann and Serdar Kuyucak},
  journal={Journal of Theoretical and Computational Chemistry},
How a mutation affects the binding free energy of a ligand is a fundamental problem in molecular biology/biochemistry with many applications in pharmacology and biotechnology, e.g. design of drugs and enzymes. Free energy change due to a mutation can be determined most accurately by performing alchemical free energy calculations in molecular dynamics (MD) simulations. Here we discuss the necessary conditions for success of free energy calculations using toxin peptides that bind to ion channels… 

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