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J. Muthukumaran

Assistant Professor, Biotechnology


I did my PhD Bioinformatics in Pondicherry Central University, Puducherry India in the year of 2013. After this I moved to Portugal for my Postdoctoral Research (2013 to 2019). Being the deep interest in computational Biology, I am involving various research areas particularly (a) Structure Based Drug Designing and Discovery, (b) Understanding the Bio-molecular interactions, (c) SNP data analysis, (d) Structural and Functional annotations of hypothetical proteins and (e) Software and Database development. I had nearly 3 years teaching and 12 years research experiences. I have published 37 international research articles in various reputed journals.


  • Teaching: 2.7 Years
  • Research: 12 Years
  • MSc.
  • MPhil.
  • PhD
Award & Recognition

  1. Appreciation Award for Poster Presentation, SBCADD – 2012 Conference, Organized by Department of Bioinformatics, Alagappa University, Karaikudi, India.
  2. Awarded the Department of Information Technology (DIT), India, Junior Research Fellowship (JRF) – October 2007 to March 2011 (Host Institute: Pondicherry University, Puducherry, India).
  3. Awarded the Council of Scientific and Industrial Research (CSIR), India, Senior Research Fellowship (SRF) - April 2011 to October 2012 (Host Institute: Pondicherry University, Puducherry, India).
  4. Awarded the Foundation for Science and Technology, Portugal, Post-doctoral Research Fellow (PDF) – December 2013 – September 2019 (Host Institute: Universidade NOVA de Lisboa (FCT-NOVA), Caparica, Portugal)


37.MUTHUKUMARAN J, Ramos J, Freire F, Paquete-Ferreira J, Otrelo-Cardoso AR, Svergun D, Panjkovich A, Santos-Silva T (2019) Shedding Light on the Interaction of Human Anti-Apoptotic Bcl-2 Protein with Ligands through Biophysical and in Silico Studies. Int J Mol Sci 20, 860.

36. Alves-Barroco C, Roma-Rodrigues C, Balasubramanian N, Guimarães MA, Ferreira-Carvalho BT, MUTHUKUMARAN J, Nunes D, Fortunato E, Martins R, Santos-Silva T, Figueiredo AMS, Fernandes AR, Santos-Sanches I (2019) Biofilm development and computational screening for new putative inhibitors of a homolog of the regulatory protein BrpA in Streptococcus dysgalactiae subsp. dysgalactiae. Int. J Med Microbiol 309, 169-181

35. Patricia Huezo-Diaz, Chakradhara Rao Uppugunduri S, J MUTHUKUMARAN, Mohamed Aziz Rezgui, Christina Peters, Peter Bader, Michel Duval, Henrique Bittencourt, Maja Krajinovic and Marc Ansari (2018) Association of CTH Variant with Sinusoidal Obstruction Syndrome in Children Receiving Intravenous Busulfan and Cyclophosphamide before Hematopoietic Stem Cell Transplantation, The Pharmacogenomics Journal 18, 64–69

34. Parthiban, A., Kumaravel, M., MUTHUKUMARAN, J., Rukkumani, R., Krishna, R., Rao, H.S.P. (2016) Synthesis, in vitro and in silico anti-proliferative activity of 4-aryl-4H-chromene derivatives. Med Chem Res 25 (7): 1308–1315

33. Kodidela S, Pradhan SC, MUTHUKUMARAN J, Dubashi B, Santos-Silva T, et al. (2016) Genotype Distribution of Dihydrofolatereductase Variants and their Role in Disease Susceptibility to Acute Lymphoblastic Leukemia in Indian Population: An Experimental and Computational Analysis. J Leuk 4:209.

32. Martins M, Baptista PV, Mendo AS, Correia C, Videira P, Rodrigues AS, MUTHUKUMARAN J, Santos-Silva T, Silva A, Guedes da Silva MF, Gigante J, Duarte A, Gajewska M, Fernandes AR (2016) In vitro and in vivo biological characterization of the anti-proliferative potential of a cyclic trinuclear organotin(iv) complex.

Mol Biosyst. 12(3):1015-23.

31. Parthiban A, MUTHUKUMARAN J, Manhas A, Srivastava K, Krishna R, Rao HS (2015) Synthesis, in vitro and in silico antimalarial activity of 7-chloroquinoline and 4H-chromene conjugates. Bioorg Med Chem Lett. 25(20):4657-63

30. J. Senthil Kumaran, J. MUTHUKUMARAN, N. Jayachandramani and S. Mahalakshmia, Synthesis, characterization, in silico DNA studies and antibacterial evaluation of transition metal complexes of thiazole based pyrazolone Schiff base, Journal of Chemical and Pharmaceutical Research, 2015, 7(4):1397-1409

29. Parthiban, A., Kumaravel, M., MUTHUKUMARAN, J., Rukkumani, R., Krishna, R., Rao, H.S.P. (2015) Design, synthesis, in vitro and in silico anti-cancer activity of 4H-chromenes with C4-active methine groups, Med Chem Res 24 (3): 1226-1240.

28. Parthiban, A., MUTHUKUMARAN, J., Moushumi Priya, A., Jayachandran, S., Krishna, R., Rao, H.S.P. (2014). Design, synthesis, molecular docking and biological evaluation of N-methyl-3-nitro-4-(nitromethyl)-4H-chromen-2-amine derivatives as potential anticancer agents. Med Chem Res, 23 (2): 642-659

27. Surekha Kanagarajan, Nachiappan Mutharasappan, Prabhu Dhamodharan, MUTHUKUMARAN JAYARAMAN, Krishna Ramadas, Jeyakanthan Jeyaraman (2014) Exploring the structural features of Aspartate Trans Carbamoylase (TtATCase) from Thermus thermophilus HB8 through in silico approaches: A potential drug target for inborn error of pyrimidine metabolism, J Biomol Struct Dyn J Biomol Struct Dyn, 32(4):591-601

26. J. Senthil Kumaran, S. Priya, J. MUTHUKUMARAN, N. Jayachandramani and S. Mahalakshmia, Synthesis, characterization and biological studies of Cu(II), Co(II), Ni(II) and Zn(II) complexes of tetradentate Schiff base ligand, Journal of Chemical and Pharmaceutical Research, 2013, 5(7):56-69

25. Manivel Panneerselvam, Kannan Muthu, MUTHUKUMARAN JAYARAMAN, Upasana Sridharan, Pranitha Jenardhanan and Krishna Ramadas (2013), Molecular Dynamic Simulations of Tubulin-Human Gamma Synuclein Complex: Structural Insight into the regulatory mechanism involved in inducing resistance against Taxol, Molecular BioSystems ,9, 1470-1488

24. J. MUTHUKUMARAN, A. Parthiban, H. Surya Prakash Rao & R. Krishna (2012), 6-Ethyl-N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E68:o180-o181

23. M. Kannan, P. Manivel , K. Geetha, J. MUTHUKUMARAN, H. Surya Prakash Rao & R. Krishna (2012), Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with Acetylcholinesterase, J Chem Biol, 5: 151-


22. Kannan Muthu, Manivel Panneerselvam, MUTHUKUMARAN JAYARAMAN, Nishith Saurav Topno, Arindam Atanu Das & Ramadas Krishna (2012), Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies, J Mol Model, 18: 4865-4884

21. P. Manivel, J. MUTHUKUMARAN, M. Kannan & R. Krishna (2011), Insight into residues involved in the structure and function of the breast cancer associated protein human gamma synuclein, J Mol Model, 17:251-263

20. J. MUTHUKUMARAN, A. Parthiban, H. Surya Prakash Rao & R. Krishna (2011), An X-ray crystallographic study of N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, J Chem Crystallogr, 41:1927–1934

19. J.MUTHUKUMARAN, A.Parthiban, P.Manivel, H.Surya Prakash Rao & R.Krishna (2011), 4--N-methyl-3-nitro-4H-chromen-2-amine, Acta Cryst. E67: o1395-o1396

18. MUTHUKUMARAN J, Karthikeyan S, Satheesh G, Manimaran, B & Krishna R (2011), Butane-1,4-diyl bis(pyridine-4-carboxylate), Acta Cryst. E67: o1803

17. MUTHUKUMARAN J, Nishandhini M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna R. & Jeyakanthan, J (2011), 4-{(4-Chlorophenyl)methyl}-4,5,6,7-tetrahydro-1,2,3-benzoselenadiazole, Acta Cryst. E67: o1421-o1422

16. MUTHUKUMARAN J, Nachiappan M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna R. & Jeyakanthan, J (2011), 1-(2-Naphthyl)-3-phenyl-3-(4,5,6,7-tetrahydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one, Acta Cryst. E67: o2010-o2011

15. MUTHUKUMARAN J, Nishandhini M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna R. & Jeyakanthan, J (2011), 3-(4-Methylphenyl)-1-phenyl-3-(4,5,6,7-tetrahydro-1,2,3-benzoselenadiazol-4-yl)propan-1-one, Acta Cryst. E67: o1660-o1661

14. J. MUTHUKUMARAN, A. Parthiban, M. Kannan, H. Surya Prakash Rao & R. Krishna (2011), 6,8-Dichloro-N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E67: o898-o899

13. J. MUTHUKUMARAN, A. Parthiban, P. Manivel, H. Surya Prakash Rao & R. Krishna (2011), 6-Methoxy-N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E67: o1276-o1277

12. J. MUTHUKUMARAN, P. Manivel, M. Kannan, J. Jeyakanthan & R. Krishna (2011), A framework for classification of antifreeze proteins in over wintering plants based on their sequence and structural features, J

Bioinform Seq Anal, 3: 70-88

11. J. MUTHUKUMARAN, P. Manivel, M. Kannan, J. Jeyakanthan & R. Krishna (2011), Advancement in computational analysis methods of plant antifreeze proteins (AFPs): An application towards classification and gene expression studies of leucine rich repeat (LRR) and ice-recrystallization inhibition domain (IRI) containing AFPs, J Comput Biol Bioinform Res, 3: 65-82

10. JAYARAMAN MUTHUKUMARAN, Mannu Jayakanthan, Sanniyasi Chandrasekar and Premendu P. Mathur (2011), Bind-Predict: An algorithm for identifying zinc fingerbinding motifs in DNA sequences, J Comput Biol Bioinform Res, 3: 91-102

9. Karthikeyan S, MUTHUKUMARAN J, Krishna R. & Manimaran, B (2011), 2,2'-diphenol, Acta Cryst. E67: o1765-o1766

8. MUTHUKUMARAN J, Kannan M, Vanitha A, Manimaran B. & Krishna R (2010), Bis(-phenyltellurido-2Te:Te)bis, Acta Cryst. E66: m558-m559

7. Vanitha A, MUTHUKUMARAN J, Krishna R & Manimaran, B (2010), Heptacarbonyl1 3C,24C-(4-phenylpyridine-1N)di--phenyltellurido-1:24Te:Te-dirhenium(I), Acta Cryst E66: m518-m5

6. Ankita Punetha, JAYARAMAN MUTHUKUMARAN, Anmol Jaywant Hemrom, Nagarajan Arumugam, Mannu Jayakanthan and Durai Sundar (2010) Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes. J Bioinform Seq Anal, 2: 1-10

5. Satyanarayana CR, Devendran A, JAYARAMAN M, Mannu J, Mathur PP, Gopal SD, Rajagopal K, Chandrasekaran A (2009), Influence of the genetic polymorphisms in the 5' flanking and exonic regions of CYP2C19 on proguanil oxidation. Drug Metab Pharmacokinet. 2009;24(6):537-48.

4. Jayakanthan M, Chandrasekar S, MUTHUKUMARAN J, Mathur PP (2009) Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for Highly Active Antiretroviral Therapy in HIV/AIDS. J Mol Graph Model. 2010 Jan;28(5):455-63

3. Jayakanthan M, MUTHUKUMARAN J, Chandrasekar S, Chawla K, Punetha A, Sundar D (2009) ZifBASE: a database of zinc finger proteins and associated resources. BMC Genomics


2. Balachandran N, Kichenamourthy S, MUTHUKUMARAN J, Jayakanthan M, Chandrasekar S, Punetha A and Sundar D (2009) Diversity of true mangroves and their associates in the Pondicherry region of South India and development of a mangrove knowledgebase. J Ecol Nat Environ 1: 99-105

1. Karthick RNS, MUTHUKUMARAN J (2008) Prediction of Three Dimensional Model and Active Site

Analysis of Inducible Serine Protease Inhibitor -2 (ISPI -2) in Galleria Mellonella. J Comput Sci Syst Biol 1: 119-125

Area of Interest

  • Bioinformatics