Major Research Project Molecular & Computational Toxicology


Course Objective

The aim is to obtain experience in scientific research including the
design and execution of experiments and to critically interpret and
reflect on the experimental results. The project will be conducted
within the field of molecular and computational toxicology, in one of
the following settings:
- University or Academic hospital
- Research institute
- Company
The internship can be performed either within the Netherlands or abroad.

Course Content

The specific content of the project depends on the available projects
and timing of the internship, but roughly deals with one of the
following areas of research:
- Biomolecular Simulation & Modeling (dr. Daan Geerke): computational
methods are developed to characterize the interaction between compounds
with different proteins and to predict their mode of binding and action.
In close collaboration with the experimental colleagues within the
division, a special focus is possible on predicting unwanted binding to
drug-safety related proteins and/or the formation of metabolites by
drug-metabolizing or biocatalytically active enzymes. The binding
affinity and -selectivity of compounds and metabolites are calculated
using efficient and accurate computational methods, and research on and
development of improved biomolecular models or force fields is possible
as well.
- Phase I and II metabolism (dr. Jan Commandeur): Research is focused on
the role of drug metabolizing enzymes, such as cytochromes P450,
glutathione transferases, sulfotransferases, and others in the
bioactivation and bioinactivation of (toxic) drugs or other chemicals
and the development of novel in vitro models for liver and kidney
- In vitro cell toxicology (Prof. dr. Paul Jennings): Utilisation of
cultured human cells, including primary cells, renal cell lines, hepatic
cell lines and induced human pluripotent stem cells for investigating
mechanisms of toxicity. Assays employed include, cytotoxicity assays,
stress assays, differentiation markers, mitochondrial injury (Seahorse
bioanalyser), barrier function, impedance (xCELLigence), fluorescent
reporter assays, transcriptomics and biokinetics.

Attention will be paid to setting up new research/experiments, using
state-of-the-art experimental or computational techniques, and data
analysis and interpretation.

Teaching Methods

Literature review, formulating a research question, conducting
experiments and/or simulation, documentation (e.g. labjournal, adherence
to protocols, appropriate meta tagging and documentation of workflows),
data analysis, reporting on results in group meetings, a written thesis
and final presentation within the research group.

Method of Assessment

Academic attitude, execution, oral presentation, and written thesis


Starting literature will be provided by the supervisor. The first 1-2
weeks of the traineeship will be spent on literature reading and
preparation for the project.

Target Audience

Research variant of the following tracks of the master Drug Discovery &
Safety: DDSA, CMCT (computational projects), DD&S (computational

Additional Information

The standard length of a major internship is 42 EC (7 months). Extension
up to 60 EC (10 months in total) can be incorporated as part of the
optional part of the master program. Make sure you discuss your personal
education plan with your master (track) coordinator well in advance. See
the “Master Drug Discovery & Safety Internship manual” for more
information (rules, regulations, tips, etc.) on the internship process.
This manual can be found on the canvas community “Master Drug Discovery
& Safety”.

Custom Course Registration

The number of internal (VU) internship positions is limited. Candidates are selected based on their motivation (in form of a motivation letter), and previous experience (outlined in CV). Please refer to the canvas site “Master Drug Discovery & Safety” for more information regarding this application procedure. Be aware that for most external positions a selection procedure applies as well. Before the start of the project an internship agreement, which includes a non-disclosure agreement has to be signed by all involved parties and the project proposal has to be approved by the VU supervisor. See the “Master Drug Discovery & Safety Internship manual” for more information on the rules and regulation regarding internships. Contact either Paul Jennings, Jan Commandeur, or Daan Geerke for specifics on the availability of projects. If after reading the manual you still have questions regarding the process related to internships, admission, approval, etc., please contact the internship coordinator via

General Information

Course Code XM_0040
Credits 42 EC
Period Ac. Year (sept)
Course Level 600
Language of Tuition English
Faculty Faculty of Science
Course Coordinator dr. D.J. Scholten
Examiner dr. D.J. Scholten
Teaching Staff

Practical Information

You cannot register for this course yourself; your faculty's education office carries out registration

Target audiences

This course is also available as: