Molecular modelling and dynamics/simulations article

The jiggling wiggling of the atoms is the basis for the existence of the life and understanding this nature of the atomic particles and various laws and phenomenon governing these is a herculean job. As Albert Einstein eloquently said once, “Nature did not deem it her business to make the discovery of her laws easy for us.” But with the rapid advancement in the field of drug discovery and in-silico drug designing, it is apposite to have better understanding of these molecular motion.

To suppress the cost and labour that was required earlier in cystallographic studies of the proteins flexibility to predict ligand binding led the researchers to seek for computational approach to solve the protein’s three-dimensional structures and interaction.

Molecular modelling is a computer based technique for determining and representing the three-dimensional structures of the molecules, also the properties associated with these 3-D structures. The main applications of molecular modelling are generation of protein structures, molecular structure visualisation, and determination of molecular properties.

Molecular dynamic simulation is a technique to study the structure-to-function relationship of macromolecules. It mimics real-life motion of atoms and molecules.

Applications: MD can be applied in understanding allostery, molecular docking and drug-designing and refining structure predictions.

a).To determine where the drug molecules bind to receptor and how they exert their effect. This information allows altering the molecule to gain different effect.

b). MD can be used for ab initio prediction of protein structure by simulating folding of the polypeptide chain from random coil.

c). To determine the functional mechanism of the proteins.

Available software packages for MD are GROMACS, AMBER, NAMD, Desmond, OpenMM and VMD (Visual Molecular Dynamics) for analyzing the results of the simulation.

GROMACS: Groningen MAchine for Chemical Simulations (GROMACS) is a free, open-source software to perform molecular dynamics, i.e. Simulate the Newtonian equations of motion for systems with hundreds to millions of particles and is widely used in the simulation of protein folding. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids, but because of its fast calculation of non-bonded interactions, it can also be used for non-biological molecules like polymers. It is operated via a command-line interface and can use files for input and output.

References:

1)Hospital A, Goñi JR, Orozco M, Gelpi J.Molecular dynamics simulations: advances and applications. Advances and applications in Bioinformatics and Chemistry. Volume 2015:8 (37-47)

2) Nadendla R R. Molecular modelling: A powerful tool for drug design and molecular docking. Springer. Volume 2014:9 (51–60)

To know more about our bioinformatics course and molecular-modelling-and-dynamics-simulations