Research @ MID Our research is focused on 1) Development of 'target' and 'small molecule' profiling systems for specific applications 2) Modeling Folding-Unfolding mechanism of proteins and 3) development of peptide based bio-nano devices. The following script is intended to give an overview of the research area we are broadly interested in, so that it will be helpful for prospective research students interested to work with us.   Chemo-informatics- Chemical Proteomics

The promise of genome sequencing was immense in revolutionizing the healthcare sector for novel diagnostic and therapeutic solutions. After complete human genome became available in public domain in 2003, this promise has become more realistic. But even where complete genome sequence is available, the information deduced about the encoded proteins were inadequate. In order to have a complete account of cell functioning, it is required to study proteins directly. This led to a more difficult task of characterizing the 'proteome', eventually resulting in the discipline of proteomics. 
 Proteins generally functions collaboratively with other proteins. Large scale study of Protein-Protein Interactions may provide an integrated view of cellular processes at the protein level. Over last few years, significant advancement have been achieved in protein separation and annotation technologies and various groups across the globe are busy inventing newer methods of analysis and innovating the existing experimental protocols. 

The property of small molecules binding to target proteins to perturb their functions has been amply exploited to produce therapeutic agents for treatment of various diseases. Understanding the full target spectrum of a drug molecule is critical to exploit the complete 'therapeutic potential' and 'toxicity' of a molecule. Our research focuses on two aspects of this drug-target interaction; 1) Simplification and abstraction of principal components responsible for pharmacological behavior, and express it in lesser dimensions for high throughput similarity search and 2) a comprehensive systems biology approach in mapping, signaling and metabolic pathways. A mass spectrometry based approach for identifying proteome wide small molecule-protein interactions have also been envisaged. In collaboration with Dr. Andreas Bender of Cambridge University UK, we have developed a 'clock model' for the virtual activity profiling of molecules by 1D fingerprinting. We plan to extend the core concept of reduced molecular representation in mapping protein-small molecule, Protein-protein interaction and studying drug promiscuity in future years. Computational Biology  Understanding the molecular mechanism of protein mis-folding can help in therapeutic intervention of diseases resulting from mis-folding and aggregation, improve kinetic stability of industrial and therapeutic proteins and have better directives while designing proteins de novo. In collaboration with Prof. Chris Bystroff of RPI New York, we have designed a computational protocol for complete pathway engineering of small two-state and large multi-state proteins. Computational experiments to develop a consensus hypothesis for the physical basis of protein kinetic stability is in progress.   Peptide based Bio-nano Systems  Controlled and directed self assemblies of nano-structures provide the key for fabrication of novel nano-materials and devices. Such self assembled structures can be made up from a variety of chemical molecules. Peptide based nano tubes and their assemblies have the scope for numerous chemical modifications helping to the design of molecules with pre-defined functions, and more importantly they may be bio-compatible. Short designed peptides can form assemblies in the form of tubes, spheres, fibrils and tapes in nano-scopic dimensions, and has demonstrated applications in bio-sensors, tissue engineering and development of antibacterial agents. Such peptide based bio-materials have been employed in the design of novel bio-materials with tailor made functions. We plan to design a series of unnatural peptides that can form nano-scale structural assemblies with characteristic mechanical and chemical properties.  OTHER PROJECTS   (at the final stage of completion, not to be pursued in future)  1. Protein Barcoding
2. Conformational directives for protein folding.
3. New Linux Distro for Bio-molecular modeling and simulations