Computational Peptide Design - Postdoc in de novo design of brain-targeting peptides, University of Copenhagen

We are seeking a talented and motivated postdoctoral researcher with a passion for computational peptide design to join an interdisciplinary project developing next-generation brain-targeted therapeutics for ischemic stroke. The successful candidate will use de novo design (including in-house developed methods), molecular modelling and omics-derived data to develop peptide shuttles capable of transporting therapeutic cargo across the blood–brain barrier. The position offers an opportunity to work at the interface of computational drug design, peptide chemistry, drug delivery and neuroscience.

Principal supervisor

Associate Professor Albert J. Kooistra, Department of Drug Design and Pharmacology

E-mail (preferred): albert.kooistra@sund.ku.dk, phone: +45 35 32 83 05

Project leader

Associate Professor Mie Kristensen, Department of Pharmacy

E-mail (preferred): mie.kristensen@sund.ku.dk, phone: +45 35 33 60 63

Start: 1 January 2027

Duration: 2 years as a postdoctoral researcher

Our group and research

The project is led by Mie Kristensen, and the computational postdoctoral researcher will be integrated into the Data Science for Drug Design (DSDD) research group, led by Albert J. Kooistra. The DSDD group develops and applies data-driven technologies for drug discovery and network medicine, with expertise in structural bioinformatics, cheminformatics, computer-aided drug design, research software and database development, and machine learning. The group’s research combines the systematic curation of structural, molecular and cellular data, including the development of widely used resources such as KLIFS, with the modelling of protein interactions and signalling networks. These insights are used together with knowledge-driven and machine-learning approaches to design molecules that modulate cellular signalling.

Project description

Ischemic stroke is a leading cause of death and long-term disability worldwide. Although current clinical interventions can restore blood flow to the brain, effective treatments that protect brain cells from stroke-induced damage remain unavailable. A major obstacle is the blood–brain barrier, which maintains the brain’s physiological environment but prevents most therapeutic compounds from reaching the brain at clinically relevant concentrations.

The project “Integrating omics and computational design for next generation brain-targeted stroke therapeutics”, funded by the Independent Research Fund Denmark, aims to overcome this challenge by developing peptide-based transport molecules that can deliver neuroprotective therapeutics across the blood–brain barrier.

By integrating large-scale biological data with advanced computational modelling and de novo peptide design, the project will:

• Identify and design novel blood–brain barrier-specific peptide shuttles.

• Optimise the peptides for target engagement, transport efficiency, stability and therapeutic applicability.

• Develop improved strategies for peptide synthesis and functionalisation.

• Evaluate the resulting candidates in cell-based blood–brain barrier models and preclinical models of ischemic stroke.

The postdoctoral researcher will play a central role in the computational design component of the project. This will include optimizing, further development, and application of workflows for peptide sequence generation, structural modelling, property prediction and candidate prioritisation. The researcher will work closely with experimental scientists in which computational predictions guide peptide synthesis and biological evaluation, and experimental results are used to improve subsequent designs.

The project brings together expertise in drug delivery, peptide chemistry, computational drug design and neuroscience. It is led by Associate Professor Mie Kristensen in collaboration with Associate Professors Albert Kooistra and Henrik Franzyk at the Department of Drug Design and Pharmacology, University of Copenhagen, and Professor Anna-Sophia Wahl at Ludwig-Maximilians-Universität München. The long-term objective is to establish new strategies for delivering protective therapeutics to the brain, thereby reducing stroke-related brain damage and improving patient recovery. The approaches and technologies developed through the project may also support the development of treatments for other neurological diseases in which delivery across the blood–brain barrier remains a major challenge.

Profile

We are looking for a computational designer who enjoys working at the interface of deep learning, molecular modelling, data science and experimental drug discovery. You should be comfortable handling biological data at scale, developing computational design workflows, and applying structure- and sequence-based methods to generate and prioritise novel peptides.

You will be expected to work closely with experimental scientists and be motivated by creating truly translatable computational designs that are then experimentally validated. The ideal candidate combines strong computational skills with an interest in peptide therapeutics, structural bioinformatics, and molecular recognition and transport across the blood–brain barrier.

Essential experience and skills

• A PhD in computational chemistry, computational biology, bioinformatics, biophysics, data science or a related field.
• Experience with computational design or modelling of peptides, proteins or other biomolecules.
• Experience developing reproducible computational workflows for biological or molecular data analysis.
• Ability to analyse and integrate heterogeneous biological datasets.
• Proficient programming skills in Python, including experience with code versioning using Git and GitHub.
• Strong scientific communication and collaboration skills, with excellent written and spoken English.

Desirable experience and skills

• Experience with de novo peptide or protein design.
• Experience with sequence- and structure-based molecular modelling, including structure prediction, docking or molecular dynamics.
• Experience with machine learning, generative modelling or optimisation for molecular design.
• Knowledge of peptide chemistry and properties relevant to stability, functionalisation and therapeutic development.
• Experience integrating omics or experimental data into computational design workflows.
• Knowledge of blood–brain barrier biology or brain-targeted drug delivery.
• Experience collaborating with experimental researchers in interdisciplinary teams.

The person will be required to relocate to Copenhagen and key responsibilities will include: establishing research ideas together with the principal investigator, leading their research project on a day-to-day basis, presenting research in internal meetings and international conferences, taking an active part in manuscript writing, and translating new knowledge in the subject area into research activities. There will be the opportunity to supervise more junior group members and contribute to teaching and dissemination activities.

Place of employment

The place of employment is at the department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, but will work in the DSDD group in the Center for Pharmaceutical Data Science Education (CPDSE). We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include a competitive computational core facility and modern environment. Moreover, the DSDD group is part of the cluster for Integrated Structural Biology (ISBUC), and the pharmaceutical informatics research section (link).

Terms of employment

The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 years. The starting date is the 1st of January 2027.

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Currently, the monthly salary starts at 40,000 DKK/approx. 5,350 EUR (August 2026 level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 17.1 % Cto your pension fund.

Foreign and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the Job Structure for Academic Staff at Universities 2020.

Questions

For further information, applicants may contact the principal supervisor, Associate Professor Albert J. Kooistra, e-mail: albert.kooistra@sund.ku.dk, phone: +45 35 32 83 05.

For more information on working and living in Denmark visit http://ism.ku.dk (International staff mobility) and https://www.workindenmark.dk

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Application procedure

Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore, your application must include the following documents/attachments – all in PDF format:

• Motivated letter of application (max. one page). Your motivation letter is an essential part of your application. It must clearly explain why you are applying for this specific position and why this project is the right fit for you. Highlight how your background, skills, and interests align with the research goals.

  • ️ Only applications with a clear, specific, and well-reasoned motivation will be considered

• CV incl. education, work/research experience, language skills and other skills relevant for the position.

• A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.

• List of publications.

• References and recommendations

• Link to your GitHub account

Application deadline: 20 September**, 23.59pm CET**

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in the second half of October.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Københavns Universitet giver sine knap 10.000 medarbejdere muligheder for at udnytte deres talent fuldt ud i et ambitiøst, uformelt miljø. Vi sikrer traditionsrige og moderne rammer om uddannelser og fri forskning på højt internationalt niveau. Vi søger svar og løsninger på fælles problemer og gør ny viden tilgængelig og nyttig for andre.

Kontakt

Albert Jelke Kooistra E-mail: vdc825@ku.dk

Info

Ansøgningsfrist: 20-09-2026 Ansættelsesdato: 01-01-2027 Arbejdstid: Fuldtid Afdeling/Sted: Department of Pharmacy