1. Dr. Prashantha Karunakar is an assistant professor who specializes in bioinformatics, chemoinformatics, and structural bioinformatics. His areas of expertise include NGS data analysis, protein structure-function analysis, data mining, molecular docking simulations, and software development. 2. He has published over 20 papers in peer-reviewed journals on topics like protein-ligand interactions, drug target identification, structure determination, and bioinformatics tool development. 3. Dr. Karunakar provides bioinformatics services including custom data analysis, database development, technical writing support, and small molecule or protein structure determination to solve biological problems.

1. Protein/DNAProtein/DNAProtein/DNAProtein/DNA –––– LigandLigandLigandLigand
InteractionInteractionInteractionInteraction
Dr. Prashantha Karunakar
Assistant Professor
Department of Biotechnology
100 Feet Ring Road, Banashankari 3rd Stage
PES University
Bangalore - 560085
Ph. No.: 080-26721983 ext 340
Mob: +91 810 554 7886
e-mail: prashanthakarunakar@pes.edu
https://sites.google.com/site/prashanthakarunakar/home

2. Bioinformatics
NGS analysis
Protein Structure analysis
Data mining and Database
Development
Technical writing
• NGS data analysis
NGS data analysis for comparative genomics, high-throughput polymorphism
detection,analysis of coding and non-coding RNAs and identifying mutant genes in
disease pathways.
• Protein Structure-function analysis
Analyze the contribution of amino acid mutation towards the change in protein
structure conformation and further its effect on functionality.
• Data mining and Database Development
Curate the information in custom designed formats and create an ontological database.
• Technical writing
Technical writing support involves the communication of complex information to those
who need it to accomplish some task or goal like thesis, research articles etc.

3. Chemoinformatics
Virtual Screening
Lead identification
Lead optimization
ADMET Prediction
Molecular Docking and Dynamics
Simulation Studies
Molecular Docking and Dynamics Simulation Studies
Focussed on molecular recognition process by using molecular docking and dynamics
simulation. It aims to achieve an optimized conformation for both the DNA-Ligand or
Protein-Ligand or Protein-Protein interaction such that the free energy of the overall system
is minimized.
Protein-Ligand Interaction DNA-Ligand Interaction Protein-Ligand Interaction Ligplot representation of
Protein-Ligand interaction

4. Protein and small molecule
Structure determination
Protein crystal data Analysis
and algorithm development
Structural Bioinformatics
Protein and small molecule Structure determination
Determination of crystal structure either of protein or small molecule. Support you towards
understanding the functionality of the structure by generating high quality images like the
packing diagrams etc. which helps to communicate your work to peer reviewed journals for the
publications
Data Analysis and algorithm development
With rich experience in structural bioinformatics, pioneered in data extraction from biological sequence or structural
databases and developing new methodology or algorithm to solve biological problems.
Packing diagram

5. Python Based Bioinformatics Software Development
• Bio-python is a collection of python modules that facilitate the development of python scripts for
bioinformatics applications.
• Bio-python provides reusable python modules that facilitate writing scripts for sequence manipulation,
accessing of databases using a range of data formats and execution and parsing of the results of various
molecular biology programs.
• Consequently, Bio-python enables developing scripts that can analyze large quantities of sequence data
in ways that are typically difficult or impossible with web based systems.

6. Publications
1. Nagaraj M K, Karunakar P, Inhibition of Leukocidin F of Staphylococcus aureus: An In Silico Approach, Int J Com Bio &
Bioinfo, (2016); 1(1), 16 - 20
2. Megha Vivek, Prashantha Karunakar, Evaluation of plants extracts for acetylcholinesterase inhibitory activity and GSK-3
(2016), International Journal of Advanced Scientific Research and Publications, V2-3 , 29-34
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), V1-1, page no 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 J Pharm Sci, 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, 1-10
(2015).DOI:10.3109/15376516.2015.1077361 ISSN: 1537-6516 (print), 1537-6524 (electronic)

7. 7. 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, vol. 2014, Article ID 697532, 10 pages,
2014. doi:10.1155/2014/697532
8. Shivakumar K V, Prashantha Karunakar, Jhinuk Chatterjee., 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)
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. A. 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)
Publications

8. Publications
13. C. 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. S. 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-dimethylamino-benzylidene)-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)

9. Publications
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)