Description:Life Sciences / Drug discovery - using Molecular dynamics
Abstract:Molecular dynamics is a powerful tool to investigate stability, conformational changes and atomic-level structures of bio-molecular complexes. In the last years, the rational drug design approach, based on exploring the structural complementary concept to generate specific antagonists for target molecules, has been endorsed. Knowing in detail the spatial structure of enzymes, by means of developed computational tools and help of a structural data bank, we can attempt to identify molecules whose specificity can match the active site of such enzyme, thus, leading them to become its inhibitors. The dynamical analysis of an enzyme is required in order to understand its function and interaction with inhibitors at atomic scale. Thus, theoretical models need long MD simulations in order to extract valuable information . Through those simulations, atoms and molecules motion is integrated using Newtons�s equations. The GROMACS package  is used as a fast-algorithm for MD simulations, running in parallel and using MPI Library . Grid computing, organized in a scientific workflow, according figure 1 , helps to minimize the computational time of the simulation.