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Thomas Stockner
Dr. Thomas Stockner

Center for Physiology and Pharmacology (Institute of Pharmacology)
Position: Associate Professor

ORCID: 0000-0002-7071-8283
T +43 1 40160 31215

Further Information


Membrane Transport Proteins; Membranes; Molecular Docking Simulation; Molecular Dynamics Simulation; Neurotransmitter Transporters; Sequence Alignment; Structural Homology, Protein

Research group(s)

Research interests

Membrane Transporter: Combining Simulations with Experiments

We combine experiments with computer simulations to study membrane transporters: molecular dynamics simulations are user to investigate the transport process at atomic detail; in vitro experiments are performed to study their function.

ABC transporter: The human genome codes for 48 members of the ABC protein family. Most members are membrane exporters, while four are involved in regulation of gene expression. Common to all ABC transporter are the nucleotide binding domains, which provide the driving force through ATP hydrolysis. We focus on conformational changes of the transport cycle, substrate selectivity, and coupling between ATP hydrolysis and substrate transport.

Neurotransmitter transporter: The secondary active transporter from the SLC6 family (including dopamine (DAT), norepinephrine (NET), and serotonin (SERT) or GABA transporters (GAT)) are mainly located on presynaptic neurons and glia cells. Their core physiological role is termination of neurotransmission by rapid removal of neurotransmitters from the synaptic cleft. Disregulationis associated with disorders like depression, attention deficit hyperactivity disorder, autism or bipolar disorder. We are using computational methods to investigate substrate and inhibitor binding, and the molecular details of active transport and use experimental approaches to very predictions (in collaboration with the Sitte and Freissmuth lab).

Techniques, methods & infrastructure

We use computational methods including molecular modelling, structural visualization, docking, homology modelling, sequence alignments, molecular dynamics simulations, and free energy calculations. Experiments are carried out with collaboration withing the Medical University of Vienna (the labs of Sitte, Freissmuth, Chiba and Szakacs).


  • Illuminating the TRPC3 signaling machinery (2019)
    Source of Funding: FWF (Austrian Science Fund), Stand alone projects
    Principal Investigator
  • NeuroTrans: Neurotransmitter Transporters: from single molecules to human pathologies (2019)
    Source of Funding: EU, Marie Sklodowska Curie Action: European Training Network
    Coordinator of the collaborative project
  • Energy coupling in the serotonin transporter (2018)
    Source of Funding: FWF (Austrian Science Fund), Stand-Alone Projects
    Principal Investigator
  • Transport cycle of the ABC transporter ABCB1 (2010)
    Source of Funding: FWF (Austrian Science Fund), Stand-Alone Projects
    Principal Investigator
  • Transmembrane Transporters in Health and Disease (project part leader) (2007)
    Source of Funding: FWF (Austrian Science Fund), Special Research Programmes (SFB35)
    Principal Investigator

Selected publications

  1. Khunweeraphong, N. et al., 2019. The ABCG2 multidrug transporter is a pump gated by a valve and an extracellular lid. Nature Communications, 10(1). Available at:
  2. Jayaraman, K. et al., 2018. Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain A. Schlessinger, ed. PLOS Computational Biology, 14(6), p.e1006229. Available at:
  3. Szöllősi, D. et al., 2018. Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1. Biophysical Journal, 114(2), pp.331–342. Available at:
  4. Stockner, T. et al., 2013. Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model S. Noskov, ed. PLoS Computational Biology, 9(2), p.e1002909. Available at:
  5. Jerabek, H. et al., 2010. Membrane-Mediated Effect on Ion Channels Induced by the Anesthetic Drug Ketamine. Journal of the American Chemical Society, 132(23), pp.7990–7997. Available at: