Assessment of Computational Methods for Ligand Binding
Popular Abstract in English Proteins are a big biological molecules that help cells to function. Proteins play important roles in all vital processes of the living cell, transporting molecules, speeding up chemical reactions, supporting structure of other proteins and the cell, helping the cell to move. Various disease-causing agents (e.g. bacteria and viruses) are constant threat to us. It is thMost drugs act on biomacromolecules. The Cost of developing new drugs is very high. A method to accurately predict binding affinities would be very useful. We have studied molecular mechanics with generalised Born and surface--area solvation (MM/GBSA) and alchemical free energy perturbation methods (FEP) for use in calculations of ligand binding energies. For the MM/GBSA method we have tested: Ca
