Prashantha Karunakar

Dr.Prashantha Karunakar. ID-WF-1341

Dr. Prashantha Karunakar

Assistant Professor

Dr. Prashantha Karunakar is an Assistant Professor of the Department of Biotechnology at PES University.

Brief Profile:

Dr. Prashantha Karunakar obtained his Masters in Bioinformatics from Kuvempu University and Ph.D degree from PES Institute of Technology (Affiliated to Kuvempu University, Shankarghatta). He worked on the Ph.D research topic titled “Crystal structure and molecular docking analysis of furan derivatives having pharmaceutical significance and determination of assembly of chains in protein targets”. Prior to joining PESIT, he worked as Research Associate at Indgen Life Technologies, Bangalore and Research Assistant at Vittal Mallya Scientific Research Foundation, Bangalore where he contributed by performing target identification, validation and docking studies of different ligands for their pharmaceutical significance. He worked at two famous international synchrotron facilities like DESY, Hamburg, Germany and ESRF, Grenoble, France where he contributed on automating the number of monomers in the asymmetric unit of protein crystal and analysis of X-ray data and resulting structure from UV induced radiation damage phasing. He has published more than 20 articles in National and International Journals. Solved two protein crystal structures of Histidine kinases during the stay at Hamburg, Germany. He is the recipient of the prestigious EMBO Practical Course on Computational Structural Biology 07-11 April 2014, at the European Bioinformatics Institute, Hinxton, UK with complete travel support. He has completed a course on Symmetry in the Solid State conducted by Prof. T. N. Guru Row at Solid State Structural Chemistry Unit, Indian Institute of Science (IISc), Bangalore, India. He is also the Editor-in-chief for International Journal of Computational Biology and Bioinformatics, Strings Publications and Scientific Advisor for DNAskew Analytics Pvt Ltd.

  • Departmental IQAC Coordinator
  • Organizing and coordinating various workshops, distinguished lectures, seminars at department level.
  • Board of Examiners, DSCE, Bangalore, BMSCE, RVCE, SIT, Tumkur, JSS, Mysore
  • Project Examiner, DSCE, RVCE
  • Guided several academic and research projects, many of them leading to research publications for UG and PG students.
  • Delivered lectures on “Protein crystallography and hands on Proteomics tools” in the Department of Biotechnology, Garden City College, Bangalore, India on 5/3/2014.
  • Organized a workshop on "Next Generation Sequencing (NGS) data analysis" in the Department of Biotechnology, PES University, Bangalore during 03-2015 & 10/2014
  • Delivered lectures on “Protein-Ligand Docking" in the Department of Biotechnology, New Horizon College of Engineering, Bangalore, India on 4/14/2013.
  • Delivered lectures on “Protein structure prediction (Secondary and tertiary) and Protein Docking" in National Bureau of Agriculturally Important Insect (NBAII), Bangalore, India on 11/29/2012.

Subjects Taught
Postgraduate Courses:
Essential Bioinformatics, Chemoinformatics and Computational Medicinal Chemistry, Proteomics, Biomolecular Modeling & Simulation

Undergraduate Courses:

Drug Design and Toxicology, Bioinformatics, Biochemistry, Bioenergetics & Metabolism, Structural Biology, Biopython (Special topic), Protein engineering and In silico drug design

Awards and Honors
EMBO fellowship to participate practical course on Computational Structural Biology - from data to structure to function”, EMBL-EBI, Hinxton, UK            on 07-11, April 2014.

Scholarship Awarded by 'National Level Scholarship Program' during Master's studies

Industry and Journal Interactions

  • Scientific Advisor - DNAskew Analytics Pvt Ltd (
  • Editor-in-chief, International Journal of Computational Biology and Bioinformatics (IJCOB)

Research areas of Interest: Bioinformatics, Computer Aided Drug Design, Molecular Modeling & Structural Bioinformatics, Crystallography

Journal Reviewer: IEEE/ACM Transactions on Computational Biology and Bioinformatics,  Asian Journal of Microbiology and Biotechnology, British Journal of Pharmaceutical Research, Chemical Science International Journal, Bioinformatics and Biology Insights

Current Research Projects

  • Successfully completed the prototype development of TEQIP sponsored project on "ChemDetect: A microcontroller based detection method for identifying and storing chemicals in the stock room"
  • Synthesis, molecular characterization and docking studies of schiff based organic compounds towards pharmaceutical significance
  • Determining the Number of Molecules (chains) in the Asymmetric Unit of a Protein using machine learning
  1. Bhimashankar B. Molkere, M. Veerabhadraswamy, Prashantha Karunakar. Synthesis and Evaluation of Biological Activities of Triazoles. J Pharm Chem Biol Sci 2016; 4(4): 512- 521
  2. Megha Vivek, Prashantha Karunakar. Evaluation of plants extracts for acetylcholinesterase inhibitory activity and GSK-3. International Journal of Advanced Scientific Research and Publications, 2016; 2(3): 29-34 (ISSN-2454–9878)
  3. Tanashree Kalghatgi, Vishaly K, Divya MS, Prashantha Karunakar, Evaluation of Antioxidant, Antimicrobial and Anti-breast Cancer Activity of Butea monosperma, Nigella sativa and Centella asiatica: An in vitro and in silico approach, International Journal of Computational Biology and Bioinformatics, 2016; 1(1): 01-06
  4. Manjegowda D S, Karunakar P, Ramachandra N B. Effect of structural changes in proteins derived from GATA4 nonsynonymous single nucleotide polymorphisms in congenital heart disease. Indian Journal of Pharma and Science, 2015; 77:735-41 (ISSN 0250-474X)
  5. K S Kiran, M K Kokila, Guruprasad R, Prashantha Karunakar, M A Pasha, Lokanath N, Naveen S. Crystal and Molecular docking studies of 3-[Bis-(2-hydroxy-4,4-dimethyl-6-oxo-cyclohex-1-enyl)-methyl]benzonitrile with focal adhesion kinase inhibitors.  Der Pharma Chemica, 2015: 7(9):268-273 (ISSN 0975-413X)
  6. Krithika, R., Jyothilakshmi, V., Prashantha, K. & Verma, R.J. Mechanism of protective effect of phyllanthin against carbon tetrachloride-induced hepatotoxicity and experimental liver fibrosis in mice. Toxicology Mechanisms and Methods, 2015: 25(9): 708-17 ISSN: 1537-6516 (print), 1537-6524 (electronic)
  7. Shivakumar K V, Jhinuk Chatterjee, Prashantha Karunakar. Inhibition of NarL of Mycobacterium tuberculosis: An in silico approach. Interdisciplinary Sciences: Computational Life Sciences, Springer Publications 2014; 6:1-8 (print ISSN: 1913-2751)
  8. Prashantha Karunakar, Chamarahalli Ramakrishnaiyer Girija, Venkatappa Krishnamurthy, Venkatarangaiah Krishna, and Kunigal Venugopal Shivakumar. In Silico Antitubercular Activity Analysis of Benzofuran and Naphthofuran Derivatives. Tuberculosis Research and Treatment, 2014, vol. 2014, Article ID 697532, 10 pages, (ISSN: 2090-1518)
  9. Prashantha Karunakar, V. Krishnamurthy, C. R. Girija and V. Krishna. Crystal Structure and Molecular Docking Analysis of Difurfurylidene Succinic Acid With Cyclooxygenases. International Journal of Pharma and Bio Sciences, 2013: 4(3): (B) 912 – 921 (ISSN 0975-6299)
  10. J. Yamuna, P. Karunakar,C. R. Girija, V. P. Vaidya and V. Krishnamurthy. Ethyl 3-amino-5-bromo-1-benzofuran-2-carboxylate. Acta Crystallographica Section E, 2013; E69, o775 (ISSN 1600-5368)
  11. Bhattacharjee, Biplab., Rose Mary Simon., Chaithra Gangadharaiah., Prashantha Karunakar. Chemogenomics Profiling of Drug Targets of Peptidoglycan Biosynthesis Pathway in Leptospira interrogans by Virtual Screening Approaches. Journal of Microbiology and Biotechnology, 2013; 23(6), 779-784 Online ISSN: 1738-8872   Print ISSN: 1017-7825
  12. Prashantha Karunakar, V.Krishnamurthy, C. R. Girija, V. Krishna,V. P. Vaidya and A. J. Yamuna. Ethyl 5-bromo-3-ethoxycarbonylamino-1-benzofuran-2-carboxylate. Acta Crystallographica Section E, 2013; E69, o342 (ISSN 1600-5368)
  13. R. Girija, S. Shalini, M. M. Jotani, K. Prashantha, K.N.Venugopala and T.V. Venkatesha. Semi-empirical Quantum Chemical calculations and Hirshfeld Surface Analysis in 2,6-Bis(2-Furanyl methylidene) cyclohexanone. conference proceedings of National Conference on ‘Challenges and Opportunities for Chemical Sciences in 21st Century’ 2013, 7-14 (ISBN: 978-81-923301-9-8)
  14. Shalini, C. R. Girija, Prashantha Karunakar, M. M. Jotani, K.N. Venugopala, T V Venkatesh. Synthesis, Characterisation, Docking Analysis and Biological Evaluation of a,a’-bis(p-dimethylamino­benzylidene)-γ-methylcyclohexanone. Indian Journal of Chemistry (Section B), 2013; 52B: 282-288. ISSN (Online 0975-0983; Print 0376-4699)
  15. Prashantha Karunakar, V Krishnamurthy, C R Girija, V Krishna, D E Vasundhara, Noor Shahina Begum, Akheel Ahmed Syed. In silico Docking analysis of Piperine with Cyclooxygenases. Journal of Biochemical Technology, 2012; 3(5): S122-127. (ISSN : 0974-2328)
  16. Biplab Bhattacharjee, Jhinuk Chattejee, Prashantha Karunakar. A Comparative Reverse Screening Approach to Identify Potential Anti-neoplastic Targets of Saffron Functional Components and Binding Mode. Asian Pacific Journal of Cancer Prevention, 2012; 13(11): 5605-5611. (ISSN: 1513-7368)
  17. Preu, J, Panjikar S, Morth P, Jaswal R, Karunakar P, Tucker P A. The sensor region of the ubiquitous cytosolic sensor kinase, PdtaS, contains PAS and GAF domain sensing modules. Journal of structural Biology, 2012; 177: 498–505. (ISSN: 1047-8477) (PDB ID’s deposited: 2YKH, 2YKF)
  18. Prashantha Karunakar, Venkatappa Krishnamurthy, Chamarahalli Ramakrishnaiyer Girija,Venkatarangaiah Krishna, Dindare Eswarappa Vasundhara, Noor Shahina Begum, Akheel Ahmed Syed. Molecular interaction of fenvalarate with actin. Bioinformation, 2011; 7(5): 234-238. ISSN (Online 0973-2063; Print 0973-8894)
  19. Prashantha Karunakar, B. S. Ravindranath, W. A. Sadik Ahmed. Computational Approach to Design a Potential Inhibitor for HIV and Mycobacterium. Advanced biotech., 2010; 10(4): 23-25 ISSN (Online 2319-6750; Print  0973-0109)
  20. Dinesh S.M, Prashantha Karunakar, C. Amruthavalli, Nallur B Ramachandra. Analysis and Homology Modeling of Proteins Derived from NKX2.5 Non-synonymous Single Nucleotide Polymorphisms Involved in Congenital Heart Disease. Nature and Science. 2010; 8(9):27-38. (ISSN: 1545-0740)
  21. Girija CR, Karunakar P, Poojari CS, Begum NS, Syed AA. Molecular Docking Studies of Curcumin Derivatives with Multiple Protein Targets for Procarcinogen Activating Enzyme Inhibition. Journal of Proteomics and Bioinformatics, 2010; (3): 200-203. (ISSN:0974-276X)