Structural Biology

Molecular Modelling and Dynamics

Molecular modelling involves the hypothetical and computational procedures which are wont to mimic the behavior of macromolecules. Molecular Modelling techniques are utilized in various fields a number of which are drug design, computational chemistry, materials science and computational biology. These methods are used for studying and understanding the properties of the molecules. One among the main applications of molecular modelling is molecular simulation. This is often the technique which uses powerful lculatiocomputers to simulate the interactions between atoms and to know the properties of materials. Such simulations involve methods that range from very detailed quantum mechanical cans on atoms to coarse-grained classical dynamics of huge groups of molecules on a timescale of milliseconds or longer.

Molecular dynamics (MD) deals with the study of physical movements of the atoms and molecules using simulation method, so it's mentioned together of the sort of N-body simulation. The atoms and molecules are allowed to interact for a hard and fast period of your time, giving a view of the dynamic evolution of the system. The trajectories of atoms and molecules are commonly determined by solving them numerically using Newton’s equations of motion for a gaggle of collaborating particles. The forces between the particles and their potential energies are calculated using inter-atomic potentials or molecular mechanics force fields. Steered molecular dynamics (SMD)

• Potentials in ab-initio methods
• Hybrid QM/MM
• Protein folding
• Enzyme catalysis
• Protein stability
• Molecular recognition of proteins
• DNA and membrane complexes