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Reaction mechanism of metalloenzymes studied by theoretical methods

Metalloenzymes catalyse a wide variety of reactions in nature. In the thesis, I have studied the reaction mechanism of three metalloenzymes, viz. [NiFe] hydrogenase (H2ase), dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase (FDH), by theoretical methods, namely quantum mechanics (QM), combined quantum mechanical and molecular mechanics (QM/MM), as well as QM/MM thermodynamic cycle per

Assessment of Computational Methods for Ligand Binding

Most 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