Erstellt am 7. Juni 2026
PhD student in the "Quantum Biology and Computational Physics" (QuantBio) group
Carl von Ossietzky Universität Oldenburg
Oldenburg 26129, Germany
Vollzeit
Reference: 1961118317
About us:
The QuantBioLab group is searching for a highly motivated PhD candidate to further develop and expand our Automated Ligand Searcher (ALISE), a virtual screening workflow embedded in the VIKING web platform. VIKING ( www.viking-suite.com ) is an interactive, online computational modelling environment that enables researchers to easily design, execute, and monitor state-of-the-art molecular simulations on high-performance computing (HPC) infrastructures without requiring advanced scripting expertise. ALISE currently provides a hierarchical screening strategy to estimate binding affinities of ligands to protein receptors using increasingly rigorous methodologies (Molecular Docking → Molecular Dynamics → Free Energy Perturbation). By combining speed and accuracy in a stepwise manner, ALISE enables efficient identification of high-potential binders from large chemical libraries. Building on previous success stories within our group, we aim to significantly extend the capabilities, flexibility, and accessibility of the platform.
A first major objective of the project will be the implementation of customizable and user-defined workflows, allowing researchers to tailor screening strategies to specific biological targets and research questions. Planned extensions include advanced ligand generation modules, fragment-based growing and linking strategies, integration of machine-learning-assisted scoring functions, automated chemical space exploration, and improved prioritization algorithms. Furthermore, the project will focus on enhancing reproducibility, scalability, and user accessibility, broadening the platform's applicability to both academic and industrial users.
Beyond methodological development, the project offers the opportunity to work at the interface of computational chemistry, structural biology, and artificial intelligence. The successful candidate will gain hands-on experience with cutting-edge virtual screening software, high-performance computing environments, workflow automation, and large-scale data analysis. Existing collaborations with experimental groups will allow additional verification of designed ligands in the laboratory. The PhD project will contribute to advancing computer-aided drug discovery (CADD) pipelines and will provide immediate value to the scientific community by making robust and high-quality design methodologies easily accessible, reproducible, and scalable. Existing collaborations with experimental groups will allow additional verification of designed ligands in the laboratory.
Your tasks:
In pursuing a doctoral degree within our group, the candidate will develop expertise in:
The candidate will be encouraged to actively present their work at leading national and international conferences, build collaborations, and engage with both academic and industrial partners. The position offers a stimulating interdisciplinary research environment, close supervision, and opportunities to shape the future direction of an actively used computational drug discovery platform.
Your profile:
Recruitment requirements are:
We offer:
Our standards:
The University of Oldenburg is dedicated to increase the percentage of female employees in the field of science. Therefore, female candidates are strongly encouraged to apply. In accordance to § 21 Section 3 NHG, female candidates with equal qualifications will be preferentially considered. Applicants with disabilities will be given preference in case of equal qualification.
Further information:
The Quantum Biology and Computational Physics group is headed by Prof. I. Solov'yov.
The position serves for personal scientific qualification (doctorate).
The QuantBioLab group is searching for a highly motivated PhD candidate to further develop and expand our Automated Ligand Searcher (ALISE), a virtual screening workflow embedded in the VIKING web platform. VIKING ( www.viking-suite.com ) is an interactive, online computational modelling environment that enables researchers to easily design, execute, and monitor state-of-the-art molecular simulations on high-performance computing (HPC) infrastructures without requiring advanced scripting expertise. ALISE currently provides a hierarchical screening strategy to estimate binding affinities of ligands to protein receptors using increasingly rigorous methodologies (Molecular Docking → Molecular Dynamics → Free Energy Perturbation). By combining speed and accuracy in a stepwise manner, ALISE enables efficient identification of high-potential binders from large chemical libraries. Building on previous success stories within our group, we aim to significantly extend the capabilities, flexibility, and accessibility of the platform.
A first major objective of the project will be the implementation of customizable and user-defined workflows, allowing researchers to tailor screening strategies to specific biological targets and research questions. Planned extensions include advanced ligand generation modules, fragment-based growing and linking strategies, integration of machine-learning-assisted scoring functions, automated chemical space exploration, and improved prioritization algorithms. Furthermore, the project will focus on enhancing reproducibility, scalability, and user accessibility, broadening the platform's applicability to both academic and industrial users.
Beyond methodological development, the project offers the opportunity to work at the interface of computational chemistry, structural biology, and artificial intelligence. The successful candidate will gain hands-on experience with cutting-edge virtual screening software, high-performance computing environments, workflow automation, and large-scale data analysis. Existing collaborations with experimental groups will allow additional verification of designed ligands in the laboratory. The PhD project will contribute to advancing computer-aided drug discovery (CADD) pipelines and will provide immediate value to the scientific community by making robust and high-quality design methodologies easily accessible, reproducible, and scalable. Existing collaborations with experimental groups will allow additional verification of designed ligands in the laboratory.
Your tasks:
In pursuing a doctoral degree within our group, the candidate will develop expertise in:
- Computational molecular design and free energy calculations
- Molecular dynamics simulations and enhanced sampling methods
- Machine learning approaches for molecular property prediction
- Workflow engineering and agent-assisted coding
- Research data management and reproducible science
- Scientific communication and publication in high-impact journals
The candidate will be encouraged to actively present their work at leading national and international conferences, build collaborations, and engage with both academic and industrial partners. The position offers a stimulating interdisciplinary research environment, close supervision, and opportunities to shape the future direction of an actively used computational drug discovery platform.
Your profile:
Recruitment requirements are:
- hold a qualifying university degree (diploma, master or similar) in physics, physical chemistry / chemical physics / biophysics, or a related field
- basic programming skills
- be highly motivated to conduct research using theoretical and computational physics methods
- have excellent English language skills (both spoken and written)
- be able to travel internationally on a regular basis, e.g. to attend regular project meetings, conferences and training activities
- be able to work in an international environment, be highly motivated and reliable, be able to meet strict deadlines
- have proven experience of using software tools for computer simulations (e.g. quantum chemistry calculations, molecular dynamics, etc.)
- have experience in handling protein structures and protein-ligand interactions
- have laboratory experience in protein biochemistry in case of experimental validation
- have experience with free energy calculations
We offer:
- Integration into a dedicated team and an excellent scientific environment
- Intensive support during your doctorate
- Payment according to collective agreement (TVL) incl. annual special payment
- Possibility of a company pension scheme (VBL) and capital-forming benefits
- 30 days of vacation
- Family-friendly working conditions with flexible working hours
- A wide range of further training opportunities as well as company health promotion services and participation in the university sports program
- Use of the VBN JobTicket
Our standards:
The University of Oldenburg is dedicated to increase the percentage of female employees in the field of science. Therefore, female candidates are strongly encouraged to apply. In accordance to § 21 Section 3 NHG, female candidates with equal qualifications will be preferentially considered. Applicants with disabilities will be given preference in case of equal qualification.
Further information:
The Quantum Biology and Computational Physics group is headed by Prof. I. Solov'yov.
The position serves for personal scientific qualification (doctorate).
