Research Activities in Bioinformatics
Its an age of nanomaterials. With the vast potential scope of application offered by one dimensional nanomaterial like carbon nanotubes (CNTs) and boron nitride (BNNTs), tremendous advancements especially in the field of Biomedical Research including Biosensing, cancer cell targeting and intracellular drug delivery have been foreseen. The interactions of anticancer drugs like Cisplatin, carboplatin, Paclitaxel, methotrexate, and anti -inflammatory drugs like nimesulide with CNTs are well studied.
We have shown the interaction of Pyrazinamide drug functionalized carbon and boron nitride nanotubes with pncA protein by molecular dynamics and density functional approach.
In the continuation, a detailed molecular dynamics simulation analysis of graphene- mediated pyrazinamide drug delivery onto the same protein has been reported. The performed analysis is able to capture the significant non-bomded interactions of drug with amino acids of proteins functional site. The energetics parameter displays the involvement of non-covalent interactions towards the observed stability of the system.
NC prime or Nc'(Effective number of codons prime) is a widely used method to measure the codon usage bias in organisms. The original formula of Nc' does not estimate accurately the codon usage bias in coding sequences in which synonymous codons for low abundant amino acids are non random. To mitigate this problem, a modification in the Nc'(mNc') has been developed at our department to more accurately measure the codon bias in coding sequences.
For the first time a web portal has been developed to calculate mNc', which is available at http://agnigarh.tezu.ernet.in The other work involves in this direction is analysis of codon usage bias in archaea, the third domain of life. As Archaea belonging to the different domain of life that grows in extreme condition, we found out favoured codons (FCs) in genomes by comparing codon usage bias between the high expression genes and the whole genomes . Neither genomic tRNA gene composition nor genome G+C% was able to explain this departure observed in phylum Crenarchaea. Future research will reveal the selection machanism causing the deviation of FCs rule in the high expression genes in Crenarchaea.
We are trying to investigate the functioning of IDPs, pathways of protein aggregation mechanism in neurodegenerative diseases like Alzheimer's , Parkinson's etc. and also the features of protein-RNA interactions using computational techniques.
Protein inverse folding problem is a natural inverse problem to protein structure prediction: given a target structure in three dimensions, we desire to design an amino acid sequence that is likely to fold to the given structure. We have been investigating certain diseases that occur due to aggragation of protein thus render it functionless, and then we are trying to generate new sequences that will fold into native protein structure with its functionality intact.