Sonika Bhatnagar

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  • Profile
  • QualificationsPh.D (Biophysics), A.I.I.M.S
  • DesignationAssociate Professor
  • DivisionBiotechnology
  • Contact No.+911125000110


I finished my Ph.D. and Post-Doctoral work in Department of Biophysics, AIIMS in 2002. Subsequently, I have been associated with the B.E. Biotechnology Program since the very early stages. During the early years, I was involved with the approval of course and development of basic infrastructure of the Divisional labs. Currently, I am developing a Computational and Structural Biology Lab. for research and teaching. I have been awarded the Innocentive solver award for Identification of top five therapeutic targets for treatment of obesity (
My research interests lie in the application of Computational and Structural Biology tools for gaining insights into Cardiovascular Disease and Bacterial Stress response with a long term focus on Drug target selection, Drug design and Repurposing. Our work has also featured as Invited commentary on International Atherosclerosis Society Website (

Areas of Interest
  • 5. Cardiovascular Disease and Bacterial Stress response:

  • Molecular mechanisms of disease, Target selection;

  • Drug Repurposing and design. 

  • Peer reviewed publications/book chapters

  1. Modeling of Plasmodium falciparum Telomerase Reverse Transcriptase Ternary Complex: Repurposing of Nucleoside Analog Inhibitors (2014) Mohanty P, Gupta A, and Bhatnagar S. Drug Repurposing, Rescue, and Repositioning. Epub.
  2. Integrative analysis of ocular complications in atherosclerosis unveils pathway convergence and crosstalk (2014) Gupta A, Mohanty P, Bhatnagar S. J Recept Signal Transduct Res. Jul 23:1-16.
  3. Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides (2014) Verma S, Kumar S, Gupta VP, Gourinath S, Bhatnagar S, Bhatnagar R Epub J Biomol Struct Dyn.
  4.  Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis (2014) Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. FEBS Open Bio. 4: 65-76. 
  5. Linkage, Mobility, and Selfishness in the MazF Family of Bacterial Toxins: A Snapshot of Bacterial Evolution (2013) Chopra N, Pathak A, Bhatnagar R, Bhatnagar S. Genome biol and evol 5, 2268-2284. 
  6. Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. Bedi SK, Prasad A, Mathur K, Bhatnagar S. (2013) J Vector Borne Dis. 50,188-96.
  7.  Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function (2011) Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. J Comput Aided Mol Des. 25, 275-91. 
  8. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach (2011) Bhatnagar S, Mishra S, Pathak R. J Recept Signal Transduct Res. 31, 75-84.
  9.  The PemK Toxin of Bacillus anthracis is a ribonuclease: An insight into its active site, structure and function. (2010) Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R J. Biol. Chem. 285, 7254-70.
  10. Mechanisms underlying the opposing effects of P2Y receptors on the cell cycle. (2008) Pathak R, Bhatnagar S, Dubey AK. J Recept Signal Transduct Res. 28, 505-29.
  11. Bhatnagar, S., Srivastava, D., Jayadev, M. S. K. and Dubey, A. K. (2006) Molecular variants and derivatives of insulin for improved glycemic control in diabetes. Prog. Biophys. Mol. Biol. 91, 199 – 228.
  12. Rao GS, Bhatnagar S. (2003) In silico structure-based design of a potent, mutation resilient, small peptide inhibitor of HIV-1 reverse transcriptase. J Biomol Struct Dyn., 21, 171-8
  13.  Rao GS, Bhatnagar S, Ahuja V. (2002) Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach. J Biomol Struct Dyn. 20, 31-8. 
  14. Bhatnagar S, Rao GS. (2000) Molecular modeling of the complex of endothelin-1 (ET-1) with the endothelin type A (ET(A) receptor and the rational design of a peptide antagonist. J Biomol Struct Dyn. 17, 957-64. 
  15. Gita Subba Rao, Sonika Bhatnagar, Vivek Ahuja, Mohd. Imran Siddiqui and Himanshu Tandon. (2000) Structure-based design of a novel peptide inhibitor of HIV-1 reverse transcriptase J. Hum. Virology 3, 262.
  16. Bhatnagar S, Rao GS, Singh TP (1995) The role of dehydro-alanine in the design of peptides. Biosystems. 34, 143-8. 
  17. Denoising, Clustering, Classification and Representation of Microarray Data for Disease Diagnostics by Bharadwaj N, Wadhwa S, Goel P, Sethi I, Arora CS, Goel A, Bhatnagar S and Parthasarathy H in “Research Developments in Computer Vision and Image Processing: Methodologies and Applications”. Editors: Srivastava R,   S. K. Singh, Dr. K. K. Shukla, IIT, BHU, Pubs: IGI Global, USA. 
  18. Introduction to Bioinformatics. Sonika Bhatnagar and A.K. Dubey in Niscair e-book on Recombinant DNA Technology and Biotechnology available online at:
  19. Emerging infectious diseases in humans MSK Jayadev, D. Srivastava, Sonika Bhatnagar, and A.K.Dubey in Microbes for Human life. Editor: Ajit. K. Verma 2007
  20. Genomics in Pathogenicity and Diversity of Flaviviruses. Sonika Bhatnagar, MSK Jayadev and A.K.Dubey in "Microbial Diversity" Eds. T. Satyanarayan and B.N.Johri. 2004, 1075-1096.


  • Invited talks
    1. “Network based insights into biological systems” in Interdisciplinary Conference on the Science and Applications of Networks held at Shiv Nadar University from March 20-22, 2015.
    2. “Genomics in Drug Design” in DBT and ICMR sponsored Laboratory course on Application of genomic technologies in malaria research 23rd Nov., 2012 at National Institute for Malaria Research.
    3. “Docking” Lecture and hands-on session in Summer School on Bioinformatics on 7th June, 2013 at Department of Biophysics, University of Delhi South Campus.
    4. “Structure and Evolution of the MazF family toxin Antitoxin Systems” in International conference on Recent advances in Structural Biology and Drug discovery, 11th Oct., 2014 at IIT, Roorkee.
    5. “N-Dimensional Phylogenetic Analysis: Integrating Structure, Function and Interactions with Evolution” at the first National Symposium on Biotechnology on 30th Oct., 2010 at Delhi Technological University, New Delhi.