PhD student in structure-based drug design with focus on machine learning (DDLS Research School)

Uppsala University

Application deadline

June 17, 2024

PhD student in structure-based drug design with focus on machine learning

The Department of Cell and Molecular Biology is one of the most international, broad and distinguished molecular bioscience departments in Europe. The department comprises sju research programs with about 220 employees ( The PhD position is available in Jens Carlsson’s group in the computational biology and bioinformatics programme. Jens Carlsson’s research focuses on using molecular modeling techniques to study protein-ligand interactions. The Carlsson group uses structure-based methods (e.g., molecular docking and molecular dynamics simulations) to understand protein function and to design ligands of pharmaceutically important targets, often in close collaboration with experimental groups. The Carlsson group is an international research team and is also part of the Science for Life Laboratory ( Visit the group website for more information (

The PhD student will be part of a data-driven life science research school. Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation. During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

At Uppsala University, we are looking to fill the position as PhD student in data driven cell and molecular biology. Data driven cell and molecular biology covers research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments.

Project description
The objective of the PhD project is to develop computational approaches to identify small molecule and peptide ligands that target therapeutically relevant receptors, with the vision to accelerate the drug discovery process. The project will be focused on addressing several challenges in structure-based drug design using artificial intelligence. Recently developed techniques for the prediction of the three-dimensional structures of proteins and protein-ligand complexes will be optimized for drug discovery applications. These methods will be applied to identify ligands of G protein-coupled receptors, a large family of membrane proteins involved in numerous physiological processes. By leveraging machine-learning enhanced virtual screening, the PhD student will be able to perform searches for ligands in chemical libraries containing billions of molecules. The project will be carried out in close collaboration with experimental research groups to evaluate the computational models developed in the project.

The applicant must hold a master’s degree in biology, chemistry, pharmacy, physics, computer science or within another subject which the employer considers to be equivalent. The applicant must have good ability to work independently as well as in a group. Excellent written and oral knowledge of English is required as the work takes place in an international environment.

Additional qualifications
Experience in modelling of proteins (e.g. receptors), protein structure prediction, computer-aided drug design, molecular docking, machine learning, and scientific programming is preferred, but not required.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines.

Your application should include:

  • A letter where you describe yourself, your research experience, and why you are interested in the position (maximum 2 pages).
  • A CV containing your education, other qualifications, and a description of knowledge relevant for the requirements of the position.
  • A copy of your diplomas and your master thesis.
  • Contact information to two reference persons.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as soon as possible or as otherwise agreed. Placement: Uppsala

For further information about the position, please contact: Jens Carlsson,, Tel: +46 (0)72 227 7976.

Please submit your application by 17 June 2024, UFV-PA 2024/1634.

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Uppsala University is a broad research university with a strong international position. The ultimate goal is to conduct education and research of the highest quality and relevance to make a difference in society. Our most important asset is all of our 7,600 employees and 53,000 students who, with curiosity and commitment, make Uppsala University one of Sweden’s most exciting workplaces.

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Submit your application through Uppsala University’s recruitment system.

Placement: Department of Cell and Molecular Biology

Type of employment: Full time , Temporary position

Pay: Fixed salary

Number of positions: 1

Working hours: 100%

Town: Uppsala

County: Uppsala län

Country: Sweden

Union representative: ST/TCO
Seko Universitetsklubben

Number of reference: UFV-PA 2024/1634

Last application date: 2024-06-17

Last updated: 2024-05-16

Content Responsible: Johan Inganni(