Pharmaceutical Biotechnology Research

Bio Molecular Dynamics

Molecular dynamics—the science of simulating the motions of a system of particles—applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. A particularly important application of MD simulation is to determine how a biomolecular system will respond to some perturbation. In each of these cases, one should generally perform several simulations of both the perturbed and unperturbed systems in order to identify consistent differences in the results. The function of biomolecules is dictated by their ability to change shape over the course of time, that is, their dynamics.This has been observed experimentally for a number of fundamental processes in biology including molecular recognition. Molecular dynamics (MD) and related methods are close to becoming routine computational tools for drug discovery. Their main advantage is in explicitly treating structural flexibility and entropic effects. Molecular dynamics can be used to explore conformational space, and is often the method of choice for large molecules such as proteins. In molecular dynamics the energy surface is explored by solving Newton's laws of motion for the system.