Our research can broadly be classified into two groups
(A) Classical molecular dynamics (MD) free energy simulation:
Current project deals with computational studies that involve processes such as codon reading by tRNAs in the ribosome and its relation to tRNA modifications, ligand binding in translation factors (aIF2,aIF5B, EF-Tu etc), tRNA recognition by aminoacyl tRNA synthetases, Virl RNA binding to RIG-I, DNA recognition by proteins such as AlKB, Spo0A and its derivaties, peptide membrane interactions etc.
The goal is to understand the remarkable speed and accuracy of protein synthesis by bridging the gap between the available crystal structures and biochemical experiments.
The following methods are frequently used :
(i) Free energy perturbation/Thermodynamic integration method to compute free energy change.
(ii) pka shift calculations (Poisson-Boltzmann/Linear Response Approach) to confirm the ionization state of amino acids in the protein.
(iii) Force field aspects (Polarizable vs Fixed charge) in the binding study.
(iv) Electrostatic contribution to ligand-protein binding (solving Poisson equation) and their component analysis.
(B) Electronic Structure calculations that predict the structure, properties, reactivity, bonding etc. of small molecules. Interesting aspects like aromaticity, tunneling, reaction rate, normal mode analysis are being studied.