Molecular Dynamics Simulation
Aminoacyl-tRNA synthetases are an indispensable component of ribosomal protein translational machinery and have been validated as potential drug target for malaria. The dynamic conformational landscape of Plasmodium tyrosyl-tRNA synthetase has been analysed in the presence and absence of bound ligand. All-atom simulations with cumulative time scale of microseconds show quantitative differences in the conformational diversity of this enzyme.
Computational Structural Biology
Understanding protein structure is indispensable to decipher molecular underpinning of physiological functions. Protein structure is a collection of Cartesian coordinates of atoms within the covalently connected amino-acids. I use computational methods to study 3D structures of proteins. Iterative calculation of convex hull layers in the structures have provided interesting insights in to the packing of atoms in the proteins. The figure below shows coordinates of C-alpha atoms of a proteins structure (left) and right image shows same set of coordinates colored according to different convex hull layers.
Reference: Geometric analysis of the conformational features of protein structures (BIOMAT 2015)
Computational Structural Chemistry
Natural Products (NPs) are chemical compounds that exist within the living systems. These molecules are suitable candidates for lead discovery. Molecular descriptor based evaluation of chemical space for NPs has provided interesting insights into their drug-likeliness. A details comparison of NPs from two different databases and FDA approved drugs highlights the potential for NPs as lead molecules. The figure below show the distribution of molecules based on quantitative estimation of drug-likeness (QED) in two NPs databases and their comparison with approved drugs.