You are here

Estimation of free energies of binding and changes in conformation by molecular simulations. 4490 project, 2009

The free energy of binding of two molecules is defined as the free energy difference between these molecules in the bound and the free, unbound state. This quantity can be determined experimentally through the measurement of binding constants using for instance BIAcore or microcalorimetry techniques. In simulations several schemes that involve statistical mechanics and reaction paths have been devised in order to compute free energy differences. In this project a student will study the tricks of free energy perturbation methods and will apply them in a simple model of protein and ligand. The simulations will be performed by modelling the molecules at the atomic level and with the use of Monte Carlo and Molecular Dynamics techniques.
The students involved in the the project will become familiar with computer programming, methods of molecular dynamics and Monte Carlo and concepts of statistical mechanics. Knowledge of computer programming is helpful but anot necessary. However, the student involved in the project should be willing to learn programming and to develop his/her own simple computer code.