Are you driven by curiosity about how proteins work — and equally excited about designing entirely new proteins with tailor-made properties from scratch? Do you thrive at the interface of computational modeling, molecular biology, and biophysical characterization, and are you eager to contribute to a cutting-edge research platform that brings together artificial intelligence and experimental science? If so, we invite you to join the Digital Biotechnology Lab at DTU Bioengineering as our new Protein Design and Biophysics Specialist.
You will be part of the Digital Biotechnology Lab within the Department of Biotechnology and Biomedicine (DTU Bioengineering) and will be partly physically based at DTU Arena for Life Science Automation (DALSA). Our work sits at the intersection of protein science, machine learning, and laboratory automation, and is driven by the ambition to build a fully integrated, closed-loop platform for AI-guided protein binder design and experimental validation. This project is carried out in close collaboration with Novo Nordisk as part of the Closed-Loop initiative.
The jobYour central responsibility will be to advance the development of an autonomous platform for the design, production, and biophysical characterization of protein binders. This is fundamentally a research role that demands deep engagement with both computational and experimental aspects of protein science. You will apply state-of-the-art protein AI models for the
de novo design of protein binders, working with tools such as ProteinMPNN, RFdiffusion, AlphaFold, and Boltz, and integrating them into automated computational pipelines for conditional backbone and sequence generation, structure prediction, docking, and
in silico screening. On the experimental side, you will carry out molecular biology procedures including cloning, site-directed mutagenesis, and cell-free expression of protein binders, followed by affinity purification and biophysical characterization. You will have a particular focus on quantifying protein-protein binding interactions, with hands-on experience in Flow Induced Dispersion Analysis (FIDA), including the associated protein chemistry such as fluorescent labeling of target proteins. Automation and scalability will be integral to your work: you will contribute to the design and implementation of semi-high-throughput workflows that allow systematic exploration of protein binder libraries, enabling the iterative, data-driven cycle of design, make, test, and learn that lies at the heart of the Closed-Loop platform.
Specific responsibilities include:
- Design and engineer protein binders using AI-guided computational methods, including generative protein models and pLM-based zero-shot predictions
- Develop and maintain Python pipelines for automated modeling, in silico screening, and data analysis
- Perform molecular biology procedures including cloning and site-directed mutagenesis
- Express protein binders using cell-free expression systems and perform affinity purification
- Carry out biophysical characterization of protein binding interactions using FIDA and related techniques, including fluorescent labeling of proteins
- Contribute to the development of semi-high-throughput experimental workflows integrated with the autonomous platform
- Collaborate closely with the industrial partner Novo Nordisk and contribute to the broader Closed-Loop initiative
Our expectations of youWe are looking for a candidate with a PhD in biochemistry, biophysics, biotechnology, or a closely related field. The ideal candidate combines genuine intellectual curiosity about molecular mechanisms with the practical ability to work across computational and experimental approaches. You should feel at home in both a coding environment and a wet lab, and appreciate how each perspective deepens understanding of the other.
Essential qualifications and experience:
- Strong background in protein biochemistry and biophysics, with experience in protein expression, purification, and characterization
- Practical experience with protein AI models for structure prediction and/or binder design (e.g., AlphaFold, ProteinMPNN, RFdiffusion, or equivalent)
- Proficiency in Python scripting for automation of computational analyses and data pipelines
- Hands-on experience with molecular biology techniques, including cloning and mutagenesis
- Experience with biophysical methods for quantification of protein-protein binding interactions
- Familiarity with cell-free expression systems and/or affinity purification methods
Desirable qualifications:
- Direct experience with FIDA or other solution-based binding assays, and with protein fluorescent labelling
- Experience with semi-high-throughput experimental setups and laboratory automation
- Background in MD simulations or other computational analyses of protein structure and dynamics
- Capacity and interest for mechanistic, biophysics-driven interpretation of experimental and computational data
- Experience working in interdisciplinary and collaborative project settings, ideally with industrial partners
What we offer in returnWe offer a position at the forefront of AI-driven protein science within a highly collaborative and internationally oriented environment. You will have access to state-of-the-art computational and experimental infrastructure, including DALSA’s automation platform, and work in close interaction with researchers at DTU and Novo Nordisk. The position gives significant scientific freedom and encourages the integration of fundamental curiosity-driven thinking with applied engineering goals. We place high value on scientific rigor, creativity, and open exchange of ideas, and we support professional development through internal and external training opportunities.
DTU Bioengineering is a dynamic and inclusive department with approximately 400 employees, and the Digital Biotechnology Lab offers an informal, stimulating atmosphere where new ideas are welcomed.
Salary and appointment termsThe appointment will be based on the collective agreement with the Danish Confederation of Professional Associations. The allowance will be agreed upon with the relevant union.
The position is a full-time (37 h/week) position with duration of 2 years and 8 months. Starting date is September 1, 2026. The workplace is the DTU Lyngby Campus.
Application and contactPlease submit your online application no later than
24 June 2026. Open the “Apply now” link, fill out the form and attach your motivated application, CV and exam certificates.
If you would like additional information about the position, please contact Associate Professor Timothy Patrick Jenkins at
tpaje@dtu.dk.
Applications received after the deadline will not be considered.
All interested candidates irrespective of age, gender, disability, race, religion or ethnic background are encouraged to apply. As DTU works with research in critical technology, which is subject to special rules for security and export control, open-source background checks may be conducted on qualified candidates for the position.
The Department of Biotechnology and Biomedicine (DTU Bioengineering) is an international leader in the areas of biotechnology and biomedicine. Our engineering approach to all aspects of biotechnology and biomedicine positions us as a valuable player with unique competences in a growing bio-based economy and with health systems transforming towards personalized medicine. We have a clear focus on the needs in the life science and biotech industries and point towards innovation, new businesses, and scientific services for the benefit of society. The department has extensive collaborations with national and international research units and industry. DTU Bioengineering has approximately 400 employees, of which two thirds are scientific staff. The department is located at DTU Lyngby Campus. DTU Arena for Life Science Automation (DALSA) is a cross-departmental initiative hosted at DTU Bioengineering that provides state-of-the-art automation infrastructure for life science research.DTU – For the benefit of society since 1829DTU is one of Europe's leading elite technical universities. Through research and education at an international top level, we create solutions to the major societal challenges of our time and help secure Europe's global leadership in sustainable technological development. Since Hans Christian Ørsted founded DTU almost 200 years ago, our mission has remained the same: We develop and create value through the natural and technical sciences for the benefit of society. DTU has 13,800 students, 1,600 PhD students, and 6,500 employees. We work in an international environment and have an inclusive, stimulating, and informal work culture. DTU has campuses in all parts of Denmark and in Greenland and collaborates with the best universities around the world.
