Large-scale Assessment of Molecular Docking Tools

Vor 4 Tagen

Basel, Schweiz Universität Basel Vollzeit

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

**The project**
The Schwede group is looking for an intern (~6 months) to assist in the EuroHPC LIGATE project that aims to accelerate and streamline computational approaches for protein-ligand interactions in the context of drug discovery and design. In this project, we collaborate with leading European HPC centres, research institutes and industrial partners to develop fast and reliable computational drug discovery pipelines, for example, for pandemic situations such as COVID-19.

**Your position**

Your responsibilities will be very hands-on and include implementation of our docking assessment workflow, design and development of the respective automated reporting system, and the necessary literature research. You will be working with technologies such as Slurm, Docker, pipelining and workflow management software, molecular docking, protein structure bioinformatics and chemoinformatics tools.
The two main main activities are the following:

- Assemble a workflow for assessment of a suite of docking tools. The continuous assessment will be based on newly-defined standard datasets of protein-ligand complexes.

**Your profile**
- **Good programming skills (Python)**.
- Hands-on experience in workflow generation / management (e.g. Snakemake, Nextflow) and software containerisation is a plus.
- Fluent in English.

**We offer you**

Salary and benefits are according to University of Basel standards.

In our research, we use AI methods to better guide protein modelling, analyse and visualise effects of sequence mutations in protein structure and function, characterise protein-ligand interactions and explore protein variation from an evolutionary perspective with particular interest in the dark proteome and drug discovery automation.

**Application / Contact**

- You are a Swiss or EU citizens, or holder of a Swiss C or S-permit.
- You are a non-EU citizen and a full-time student studying towards a degree that requires an internship (confirmation letter from your University will need to be provided for immigration clearance).

Apply

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