PhD fellowship in computational analysis and modelling of protein interaction
Department of Biology
Faculty of Science
University of Copenhagen The Amelie Stein group is looking for a PhD student in computational analysis and modelling of protein interaction. The PhD student will work together with other members in the Stein group as well as experimentalists in collaborating groups at UCPH and elsewhere, and other modellers in the Rosetta community. The PhD project aims to study the function of disordered proteins by combining coarse-grained molecular dynamics simulations, machine learning and bioinformatics.
The start date is expected to be 15 July 2026, or as soon as possible thereafter. Details about the project, what we are looking for and how to apply can be found below.
The project The PhD position is part of the Proteins in CONTEXT project where we aim to analyse limitations of current models for protein-protein and protein-ligand interactions, and use these insights to develop better models. The overall project combines data curation, benchmarking, and method development with classic and deep learning approaches. For background, see
https://doi.org/10.48550/arXiv.2507.17446 and
https://doi.org/10.1371/journal.pgen.1011681 as well as other publications from the group.
Who are we looking for? We are seeking applicants with a Master’s degree in bioinformatics, (bio)chemistry, data science, or similar fields. The candidate should ideally have prior research experience (for example through an MSc project) within one or more of these areas:
- Structural modelling of protein interactions and complexes with tools like AlphaFold, Boltz1/2, Rosetta
- Development or application of of machine learning or classical models for protein modelling
- Analysis, interpretation and visualisation of medium- to large-scale sets of biological data
The candidate should have a strong quantitative background.
Our group and research- and what do we offer? The Stein group studies consequences of mutations on proteins and their interactions. This PhD project is fully computational, but the group also has scientists in the wet lab and collaborates with more, leading to close integration and insights into the data generation processes. The PhD student will work in the group of Amelie Stein, located at the Department of Biology in central Copenhagen. The group is also part of an interdisciplinary and collaborative research environment at the Section for Computational and RNA Biology, and you will have the chance to interact with scientists across disciplines. The group is highly international, and a good level of spoken and written English is required.
We offer a dynamic and international research environment. Current members of the research group come from a broad range of scientific and personal backgrounds, and we value openness, collaborations, and interdisciplinary work. We are strong proponents of open science.
Inquiries about the position can be made to Associate Professor Amelie Stein, who will be the principal supervisor, at
amelie.stein@bio.ku.dk. Note that all applications must be made via the online system as described below.
The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.
The PhD programme Qualifications needed for the regular programme To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. bioinformatics or (bio)chemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.
Terms of employment in the regular programme Employment as a PhD fellow is full time and for a maximum of 3 years.
Employment is conditional upon your successful enrolment as a PhD student at the PhD School at SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.
Terms of appointment and payment according to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.
Responsibilities and tasks - Carry through an independent research project under supervision
- Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
- Participate in active research environments, including a stay at another research institution, preferably abroad
- Teaching and knowledge dissemination activities
- Write scientific papers
- Write and defend a PhD thesis on the basis of your project
We are looking for the following qualifications: - Professional qualifications relevant to the PhD project
- Relevant publications
- Relevant work experience
- Other relevant professional activities
- Good English language skills
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Application and Assessment Procedure Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.
Please include: - Curriculum vitae (max 2. pages) including information about your education, relevant experience, language skills and other skills relevant for the position
- A cover letter (max 1. page) motivating why you are interested in this position and why you would be a good fit
- Original diplomas for Bachelor and Master and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
- List of publications including preprints (if relevant). Do not attach the actual publications.
Application deadline: The deadline for applications is 12 April 2026 23:59 GMT +2
. 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 deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified whether you will be passed for assessment.
The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.
Questions For specific information about the PhD fellowship, please contact the principal supervisor Amelie Stein
amelie.stein@bio.ku.dk General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.
The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.
Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.