University of Malta

Dr Jean Paul Ebejer
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Dr Jean Paul Ebejer

Dr Jean Paul Ebejer


Centre for Molecular Medicine and Biobanking
Room 320
Biomedical Sciences Building
University of Malta
contact+356 2340 3263

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Dr Jean-Paul Ebejer read an undergraduate bachelors degree in I.T. at the University of Malta, graduating with honours in 2000. Immediately after he moved to Germany, where he worked for IBM as an IT specialist on Foreign Exchange and Money Market systems for Credit Suisse and Deutsche Bank. In 2004 he started working for Ixaris Systems, on their flagship product Entropay (, where he eventually became a technical architect. Following an MGSS scholarship and his strong interest in biological systems, data sciences, and "anything for which an explanation is in short supply" he successfully completed, with distinction, an MSc in Bioinformatics and Theoretical Systems Biology at Imperial College, London (2008-2009). He was then awarded a Marie Curie Fellowship to undertake a doctoral degree in computational drug discovery at the University of Oxford. He completed his D.Phil. in 2014 under the supervision of Prof. Charlotte Deane and Prof. Garrett Morris.

During his years in industry he has always kept a strong link with academia and has lectured a variety of technical courses. He is a keen Java enthusiast and has been an invited speaker at the Java Users Group. He finds it hard to admit that he prefers Python nowadays.

Dr Ebejer (but everyone calls him JP) has been rather concerned lately about the increasing number of media reports that the world is not going to end because of climate change, nuclear war, zombie (or alien) attack, or a second ice age, but rather because our current stock of medicines are fast becoming ineffective against evolving pathogens. As a consequence, he has used data science, bioinformatics and cheminformatics techniques to find novel, active molecules to help fight antibiotic resistance. Formally, he has done this in an ongoing EU project called Nabarsi ( He has published several papers in peer-reviewed scientific journals. He is currently employed as a Lecturer at the University of Malta and is part of the problem setting committee of the yearly ICTSA Programming Competition.

Research Interests & Publications

Research Interests

  • Bioinformatics
  • Cheminformatics
  • Computer-Aided Drug Design
  • Virtual Screening
  • Data Science (and Analytics)
  • Machine Learning
  • Big Data (& Cloud Computing)

Selected Publications

Ebejer, J., Charlton, M.H. & Finn, P.W. 2016, "Are the physicochemical properties of antibacterial compounds really different from other drugs?", Journal of Cheminformatics, vol. 8, no. 1, pp. 1-9.

Kher, S.S., Penzo, M., Fulle, S., Ebejer, J.P., Finn, P.W., Blackman, M.J. & Jirgensons, A. 2015, "Quinoxaline-Based Inhibitors of Malarial Protease PfSUB1", Chemistry of Heterocyclic Compounds, vol. 50, no. 10, pp. 1457-1463.

Kelm, S., Vangone, A., Choi, Y., Ebejer, J., Shi, J. & Deane, C.M. 2014, "Fragment-based modeling of membrane protein loops: Successes, failures, and prospects for the future", Proteins: Structure, Function, and Bioinformatics, vol. 82, no. 2, pp. 175-186.

Wilman, H.R., Ebejer, J., Shi, J., Deane, C.M. & Knapp, B. 2014, "Crowdsourcing Yields a New Standard for Kinks in Protein Helices", Journal of Chemical Information and Modeling, vol. 54, no. 9, pp. 2585-2593.

Ebejer, J., Fulle, S., Morris, G.M. & Finn, P.W. 2013, "The emerging role of cloud computing in molecular modelling", Journal of Molecular Graphics and Modelling, vol. 44, no. 0, pp. 177-187.

Ebejer, J., Hill, J.R., Kelm, S., Shi, J. & Deane, C.M. 2013, "Memoir: template-based structure prediction for membrane proteins", Nucleic acids research, vol. 41, no. W1, pp. W379-W383.

Ebejer, J., Morris, G.M. & Deane, C.M. 2012, "Freely Available Conformer Generation Methods: How Good Are They?", J.Chem.Inf.Model., vol. 52, no. 5, pp. 1146-1158.

Withers-Martinez, C., Suarez, C., Fulle, S., Kher, S., Penzo, M., Ebejer, J., Koussis, K., Hackett, F., Jirgensons, A., Finn, P. & Blackman, M.J. 2012, "Plasmodium subtilisin-like protease 1 (SUB1): Insights into the active-site structure, specificity and function of a pan-malaria drug target", International journal for parasitology, vol. 42, no. 6, pp. 597-612.


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University of Malta
L-Università ta' Malta