Subha Kalyaanamoorthy

Subha Kalyaanamoorthy
Assistant Professor
Location: ESC 234
Phone: 519-888-4567, ext. 35804


Subha Kalyaanamoorthy’s research is focused on developing and employing computational methods to address biological, health and environmental challenges.

She involves a hybrid scientific approach, where she and her research group make new novel hypothesis using in silico approaches and validate them in their wet lab.

Their research mainly engages multiple disciplines including molecular modeling and molecular dynamics simulations, Quantum modeling and simulations, protein biochemistry, machine learning, phylogenetic inference and bioinformatics to understand the structure, function, dynamics and evolution of proteins of interest. Drug discovery and synthetic biology are the key application areas of her research.

Research Interests

  • Structure- and ligand- based drug discovery
  • Biomolecular simulations
  • Membrane proteins
  • Enzymes
  • Protein structure-function evolution
  • Protein engineering
  • Computational Genomics
  • Contamination & Remediation: Water, Soil, Air
  • Carbon Dioxide Capture and Storage
  • Neuroscience
  • Biomaterials, Polymers and Bioplastics
  • Synthetic Chemistry and Catalysis
  • Bioinformatics, Systematics and Evolution
  • Drug Discovery, Design and Delivery


  • 2013 Ph.D., Computational Biology and Bioinformatics, La Trobe University, Australia
  • 2007 M.Sc., Bioinformatics, Annamalai University, India


  • 2018-2020 NSERC Canada Post-Doctoral Fellowship Award
  • 2013-2016 OCE Post-Doctoral Fellowship
  • 2012 LSCC PhD Top-up fellowship
  • 2011 Travel fellowship from the Victorian Life Sciences Computation Initiative
  • 2010-2013 La Trobe University Postgraduate Research and Full Fee Remission Scholarships
  • 2009-2010 Deakin University International Research Scholarships

Affiliations and Volunteer Work

  • Member, Waterloo Artificial Intelligence Institute


  • CHEM 233 - Fundamentals of Biochemistry
    • Taught in 2021, 2022, 2023
  • CHEM 400 - Special Topics in Chemistry
    • Taught in 2020
  • CHEM 481 - Rational Design of Potential Drug Candidates
    • Taught in 2020, 2021, 2022, 2023
  • CHEM 731 - Selected Topics in Biochemistry
    • Taught in 2022, 2023

* Only courses taught in the past 5 years are displayed.

Selected/Recent Publications

  • Wong, T.K., Kalyaanamoorthy, S., Meusemann, K., Yeates, D.K., Misof, B. and Jermiin, L.S., 2020. A minimum reporting standard for multiple sequence alignments. Nucleic Acids Research: Genomics and Bioinformatics, 2020, 2(2), iqaa024.
  • Feng T, Kalyaanamoorthy S, Ganesan A, Barakat KH, Atomistic modeling and molecular dynamics analysis of human CaV1. 2 channel using external electric field and ion pulling simulations. BBA: General Subjects, 2019, 1863(6), 1116-1126.
  • Kalyaanamoorthy S, Barakat, KH, Binding modes of hERG blockers: An unsolved mystery in drug discovery arena. Expert opinion in drug discovery, 2018, 13(3), 207-210. [Invited article]
  • Kalyaanamoorthy S, Barakat, KH. Development of safe drugs: The hERG challenge. Medicinal Research Reviews, 2018, 38(2), 525-555.
  • Kalyaanamoorthy S, Minh BQ, Wong TFK, von Haeseler A, Jermiin LS. ModelFinder: A fast model selection method that greatly improves phylogenetic estimates. Nature Methods, 2017, 14, 587- 589.
  • Wilding M, Peat TS, Kalyaanamoorthy S, Newman J, Scott S, Jermiin LS. Reverse engineering: transaminase biocatalyst development using ancestral sequence reconstruction. Green Chemistry, 2017, 19, 5375-5380.
  • View all Subha Kalyaanamoorthy's publications on Google Scholar: