PhD Position in Computer-Aided Drug Design of Carbohydrate Mimics

We invite applications for a PhD position in computer-aided drug design at the Computational Pharmacy Group, Department of Pharmaceutical Sciences, University of Basel. This position is part of an interdisciplinary project focused on the rational design of carbohydrate mimetics as antagonists of collectin-11, a key lectin in the innate immune system.

Project Overview
Collectin-11 is a pattern recognition receptor that initiates the lectin pathway of complement activation-an essential component of innate immunity. Beyond its role in pathogen defense, collectin-11 contributes to sterile inflammatory responses, such as ischemia-reperfusion injury, making it an attractive target for novel anti-inflammatory therapies.
The successful candidate will be responsible for the
in silico design and molecular modeling of carbohydrate mimics with the goal of developing potent and selective collectin-11 antagonists. These compounds will be synthesized and tested by experimental collaborators within our team. The project involves techniques such as
molecular dynamics simulations, structure-based drug design (docking, scoring, QSARs), free energy calculations,
cheminformatics workflows, and machine learning.
We are looking for a highly motivated and talented PhD student with a strong background in molecular modeling and a passion for applying computational methods to solve biologically relevant problems. The ideal candidate will demonstrate:

• A Master's degree (or equivalent) in pharmaceutical sciences, chemistry, computational biology, bioinformatics, or a related field.
• Excellent understanding of structural biology and molecular interactions, particularly in the context of protein–ligand recognition.
• Excellent understanding of structural biology and molecular interactions
• Previous experience with modeling of carbohydrates and their binding proteins is a plus.
• modeling of carbohydrates and their binding proteins
• Practical knowledge of molecular modeling tools and techniques (e.g., docking, MD simulations, FEPs, QM/MM methods).
• Programming or scripting proficiency (e.g., Python, Bash) is highly desirable.
• Strong problem-solving, analytical, and communication skills.
• Enthusiasm for interdisciplinary collaboration and innovation.

Why Basel?The University of Basel-founded in 1460-is Switzerland's oldest university and a globally recognized research institution with exceptional strength in the life sciences. Situated in the center of Europe's premier pharmaceutical and biotech hub, Basel is home to leading companies in the field, and numerous cutting-edge startups, offering unique exposure to both academic excellence and industrial innovation.

• A fully funded PhD position (Swiss National Science Foundation) of total duration of 4 years
• Access to high-performance computing resources and state-of-the-art modeling tools
• A collaborative and intellectually stimulating research environment
• Opportunities for advanced training, international conferences, and networking
• An inclusive university in a vibrant, international city

Application / Contact
 
Please send your application as a single PDF containing:

• A motivation letter
• Curriculum vitae
• Academic transcripts
• Contact information for at least two academic referees

Applications will be reviewed on a rolling basis until the position is filled. Preferred starting date is August 1, 2025.