Assistant Professor at National Institute of Technology Andhra Pradesh, India
Dr. Nisha Amarnath Jonniya is a dynamic and accomplished academician and researcher, currently serving as an Assistant Professor in the Department of Biotechnology at NIT Andhra Pradesh. With a profound expertise in computational biophysics and drug discovery, she has built a commendable research career focused on unraveling the conformational dynamics of biomolecules, particularly protein kinases implicated in various diseases. Dr. Jonniya obtained her Ph.D. from IIT Indore, where she investigated molecular modeling and simulation approaches for discovering inhibitors against hypertension-related kinases. Her professional journey spans prestigious institutions, including a current postdoctoral tenure at the University of California, San Diego under NIH funding. Her collaborative projects have addressed critical topics such as dengue virus inhibition and protein kinase regulation in Cushing’s syndrome. With over 30 high-impact publications and significant mentoring experience, Dr. Jonniya continues to contribute meaningfully to the fields of structural biology and computational drug design. Her dedication to translational research, coupled with active involvement in academic development programs and scientific outreach, underscores her commitment to both science and education.
Professional Profile
Education
Dr. Nisha Amarnath Jonniya’s academic journey exemplifies excellence and dedication. She completed her Ph.D. in Computational Biophysics from the Indian Institute of Technology (IIT) Indore, with a stellar CPI of 8.88. Her research, conducted under the guidance of Dr. Parimal Kar, focused on the conformational dynamics of kinases implicated in hypertension and involved molecular modeling and simulations to identify potent inhibitors. Prior to her doctoral studies, she earned an M.Tech in Bioinformatics from Maulana Azad National Institute of Technology (MANIT) Bhopal. Her M.Tech dissertation revolved around the application of support vector machine models for genotype classification in Hepatitis C Virus. Dr. Jonniya laid the foundation of her academic career with a B.Tech in Biotechnology from NIT Raipur, where she graduated with honors and departmental rank I. Her strong academic performance throughout her educational tenure, including top ranks at Kendriya Vidyalaya Kusmunda, reflects her consistent commitment to academic excellence and sets the groundwork for her future in high-impact research and teaching.
Professional Experience
Dr. Nisha Amarnath Jonniya’s professional experience spans prestigious institutions across India and the United States. Currently, she is serving as a Postdoctoral Employee at the University of California, San Diego (UCSD), where she is funded by the NIH to explore how disease-associated mutations affect the structure and function of Protein Kinase A. Under the mentorship of Prof. Susan Taylor, she is applying advanced computational techniques to elucidate allosteric regulations in kinases. Prior to this, Dr. Jonniya worked as a Research Associate at IIT Indore, focusing on antibody redesign and inhibitor identification against the dengue virus using in silico methods under a DST-funded project. She also served as a Lecturer at NIT Raipur from 2010 to 2015, where she taught undergraduate courses in biotechnology. Additionally, she held a teaching assistantship at IIT Indore during her Ph.D. studies. Her professional journey reflects a seamless integration of teaching, mentoring, and advanced research. Across these roles, she has contributed significantly to interdisciplinary biomedical research, mentored budding scientists, and fostered an academic environment conducive to collaborative innovation and scientific inquiry.
Research Interest
Dr. Nisha Amarnath Jonniya’s research interests lie at the intersection of structural biology, computational biophysics, and molecular drug design. Her work focuses on understanding the structural and thermodynamic properties of biomolecular systems, particularly proteins and glycans. She explores conformational dynamics using enhanced sampling molecular dynamics methods, providing insight into protein flexibility and function. A key emphasis of her research is on computational modeling of biomolecular recognition processes, including protein-protein and protein-ligand interactions, which are crucial for elucidating disease mechanisms and identifying therapeutic targets. Her projects have addressed critical biological problems, such as kinase regulation in hypertension and structural alterations in dengue virus proteins. Through structure-based drug discovery approaches, she has contributed to the identification of novel inhibitors and antibody enhancements. Dr. Jonniya’s ability to bridge theoretical modeling with translational biomedical applications underscores her long-term goal to contribute to precision medicine. Her research remains driven by the motivation to harness computational power for decoding complex biological phenomena and translating them into clinically relevant solutions.
Research Skills
Dr. Jonniya possesses a robust and versatile skill set in computational and bioinformatics tools essential for modern biomedical research. She is proficient in programming languages like Python, R, and shell scripting, and has advanced experience with molecular dynamics software such as AMBER and GROMACS. She routinely employs simulation and modeling tools like Schrodinger-Suite, Autodock, AlphaFold, UCSF Chimera, and PyMOL for structure-based drug design and protein analysis. Her skill set also includes visualization tools (VMD), plotting libraries (Matplotlib, Gnuplot), and LaTeX for scientific documentation. She has expertise in techniques such as sequence alignment, molecular docking, phylogenetic analysis, network analysis, virtual screening, and homology modeling. Dr. Jonniya is well-versed in both Windows and Linux operating systems, enhancing her adaptability across computational environments. Her command over enhanced sampling techniques, free energy calculations, and allosteric network mapping uniquely positions her for high-resolution insights into protein dynamics. These technical competencies, combined with a deep understanding of biomolecular interactions, empower her to lead impactful projects in structural biology and rational drug discovery.
Awards and Honors
Throughout her academic and professional career, Dr. Nisha Amarnath Jonniya has earned several notable accolades. She secured first rank in both her undergraduate (B.Tech in Biotechnology) and postgraduate (M.Tech in Bioinformatics) programs at NIT Raipur and MANIT Bhopal respectively, reflecting her exceptional academic abilities. She qualified the prestigious Graduate Aptitude Test in Engineering (GATE) in 2007 and was a consistent top performer from school through higher education. Dr. Jonniya received the Best Oral Presentation award at IIT Indore’s Symposium on Advances in Biosciences and Bioengineering in 2019. She has delivered invited talks and presented her research at renowned national and international platforms, including the Gordan Research Conference (USA) and Max Planck Institute (Germany). Her scientific contributions have been published in prestigious journals such as PNAS, eLife, and the Journal of Physical Chemistry B. In recognition of her expertise, she has served as a reviewer for reputed journals including ACS Omega and the Journal of Biomolecular Structure and Dynamics. These honors underscore her academic excellence, leadership in research, and ongoing contributions to the scientific community.
Conclusion
Dr. Nisha Amarnath Jonniya represents the epitome of dedication, innovation, and academic brilliance in the field of computational biology. Her multidisciplinary background, encompassing biotechnology, bioinformatics, and biophysics, has enabled her to address pressing biomedical challenges through in silico approaches. From top academic ranks to international collaborations and high-impact publications, her journey reflects a commitment to excellence and a passion for scientific inquiry. As an educator, she has not only taught and mentored students at premier institutions but also organized and participated in numerous scientific workshops and conferences, contributing to knowledge dissemination and capacity building. Her research continues to break new ground in understanding molecular mechanisms of diseases and designing targeted therapeutics. Moving forward, Dr. Jonniya is well-positioned to make transformative contributions to personalized medicine, drug development, and molecular therapeutics. Her career serves as a model for aspiring researchers aiming to blend computational skills with biological insight to tackle complex healthcare problems of the 21st century.
Publications Top Notes
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Title: Current and novel therapeutic molecules and targets in Alzheimer’s disease
Authors: A. Kumar, C.M. Nisha, C. Silakari, I. Sharma, K. Anusha, N. Gupta, P. Nair, …
Year: 2016
Citations: 191
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Title: Molecular Docking and In Silico ADMET Study Reveals Acylguanidine 7a as a Potential Inhibitor of β‐Secretase
Authors: C.M. Nisha, A. Kumar, P. Nair, N. Gupta, C. Silakari, T. Tripathi, A. Kumar
Year: 2016
Citations: 166
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Title: Docking and ADMET prediction of few GSK-3 inhibitors divulges 6-bromoindirubin-3-oxime as a potential inhibitor
Authors: C.M. Nisha, A. Kumar, A. Vimal, B.M. Bai, D. Pal, A. Kumar
Year: 2016
Citations: 119
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Title: Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations
Authors: M.F. Sk, R. Roy, N.A. Jonniya, S. Poddar, P. Kar
Year: 2021
Citations: 86
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Title: Investigating phosphorylation-induced conformational changes in WNK1 kinase by molecular dynamics simulations
Authors: N.A. Jonniya, M.F. Sk, P. Kar
Year: 2019
Citations: 51
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Title: Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM
Authors: M.F. Sk, N.A. Jonniya, R. Roy, S. Poddar, P. Kar
Year: 2020
Citations: 44
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Title: Identification of potential inhibitors against Epstein–Barr virus nuclear antigen 1 (EBNA1): An insight from docking and molecular dynamic simulations
Authors: S. Jakhmola, N.A. Jonniya, M.F. Sk, A. Rani, P. Kar, H.C. Jha
Year: 2021
Citations: 40
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Title: Immunoinformatics approach to design multi-epitope-subunit vaccine against bovine ephemeral fever disease
Authors: S. Pyasi, V. Sharma, K. Dipti, N.A. Jonniya, D. Nayak
Year: 2021
Citations: 35*
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Title: Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations
Authors: N.A. Jonniya, P. Kar
Year: 2020
Citations: 30
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Title: Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies
Authors: R. Roy, M.F. Sk, N.A. Jonniya, S. Poddar, P. Kar
Year: 2022
Citations: 23