Title:Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist’s Prospective
Volume: 18
Issue: 11
Author(s): Indu Kumari, Padmani Sandhu, Mushtaq Ahmed and Yusuf Akhter*
Affiliation:
- Structural Bioinformatics Group, Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Shahpur, District, Kangra, 176206, Himachal Pradesh,India
Keywords:
Biomolecules, force field, ligand, interactions, molecular dynamics, molecular mechanics.
Abstract: Molecular dynamics (MD) is a computational technique which is used to study biomolecules
in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule
embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The
potential energies of the atoms are explained by a mathematical expression consisting of different forces
and space parameters. There are various software and force fields that have been developed for MD
studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein
folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein
interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at
the atomic and molecular levels. However, there are still some parameters including torsions in amino
acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single
stranded nucleic acids for which the force fields need further improvement, although there are several
workers putting in constant efforts in these directions. The existing force fields are not efficient for
studying the crowded environment inside the cells, since these interactions involve multiple factors in
real time. Therefore, the improved force fields may provide the opportunities for their wider applications
on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the
basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental
biological and physiological processes at the molecular levels that may be further applied in various
fields including biotechnology, fisheries, sustainable agriculture and biomedical research.
