molecular operating environment installation directory

The simulations run for hours (sometimes days) in order to get to meaningful lengthier timescales, and gain insights on final confirmation of a molecule. We measure the performance of an MD simulation as nano-seconds per day (Ns/day). The typical time scales of the simulated system are in the order of micro-seconds (Ms) or nano-seconds (Ns).

The importance of MD came to bear on recent efforts for the SARS-COV-2 vaccine where MD applications such as GROMACS helped researchers identify molecules that bind to the spike protein of the virus and block it from infecting human cells. MD simulations are used across various domains such as material sciences, biochemistry, biophysics and are typically used in two broad ways to study a system. This work provides a brief description of a series of studies implemented in the software MOE (Molecular Operating Environment) with particular attention to the medicinal chemistry aspects.Molecular dynamics (MD) is a simulation method for analyzing the movement and tracing trajectories of atoms and molecules where the dynamics of a system evolve over time. Moreover, through this type of computational techniques and theoretical approaches, it is possible to develop explanatory hypothesis on the mechanism of action of drugs. The development of sophisticated Docking methodologies also allows a more accurate predict of the biological activity of molecules. The codification of the structural information of molecules through molecular descriptors and the subsequent data analysis allow establishing QSAR models (Quantitative Structure-Activity Relationship) that can be applied to the design and the virtual screening of new drugs. In the last years bioinformatics has experienced a great evolution due to the development of specialized software and to the increasing computer power.

For this reason the pharmaceutical industry has shown great interest in theoretical methods that enable the rational design of pharmaceutical agents. This effort arises from the large number of compounds that need to be synthesized and subsequently biologically evaluated. The search for new compounds with a given biological activity requires enormous effort in terms of manpower and cost.

Molecular operating environment installation directory