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About the Role

This position is part of an in silico Antibody–Antigen (Ab–Ag) analysis project investigating molecular interactions in rheumatological diseases. The project aims to characterize complex Ab–Ag interactions using computational approaches and expand analytical capabilities for multiple antibody–antigen systems. The successful candidate will work at the interface of bioinformatics, computational biology, and structural biology, contributing to the implementation, optimization, and scaling of established computational pipelines to support translational research objectives.

Responsibilities

Perform detailed biochemical and structural analysis of antibody-antigen interactions to uncover disease mechanisms in rheumatology
Maintain, optimize, and expand our current in silico Ab-Ag analysis pipeline
Design and implement automated high-throughput antigen search functionalities for specifically prescribed antibodies
Deploy, manage, and scale computational workflows across High-Performance Computing (HPC) clusters
Translate complex computational findings into actionable insights for downstream experimental validation

Requirements

Master’s degree (or equivalent experience) in Molecular Biology, Bioinformatics, Computational Biology, or a closely related structural science discipline
Strong foundational background intersecting biochemistry and bioinformatics
Hands-on experience with state-of-the-art structural prediction tools, specifically AlphaFold
Proven expertise running and analyzing Molecular Dynamics (MD) simulations (e.g., GROMACS, AMBER, NAMD)
Demonstrated experience developing and managing HPC pipelines (including bash scripting, workload managers like Slurm, or workflow languages like Nextflow/Snakemake)

Skills

Bioinformatics
Computational Biology
Structural Biology
AlphaFold
Molecular Dynamics (MD) simulations
GROMACS
AMBER
NAMD
HPC pipelines
bash scripting
Slurm
Nextflow
Snakemake

Location

Berlin

Work Type

Part-time
75%
29.55 hours per week

Experience Level

Based on qualifications and professional experience

Education Level

Master’s degree (or equivalent experience)

Salary/Compensations

Remuneration group 13 TV-L
Salary based on TV-L (collective agreement for the public service of the federal states) in accordance with qualifications and professional experience with annual bonus payment

Benefits

Friendly work environment
Flexible work and meeting times
Excellent equipment
Challenging professional environment
Active onboarding process
Professional training opportunities
Support in professional development
Additional pension scheme (VBL)
30 days annual leave
Flexible working hours (flexitime)
Capital allowance of up to €150 per month
BVG job ticket plus the remaining balance
Use of canteens and sports programs of the Freie Universität Berlin (FUB) at reduced rates

About the Company

The Zuse Institute Berlin (ZIB) is an interdisciplinary research institute for applied mathematics and data-intensive high-performance computing.
Its research focuses on modeling, simulation and optimization with scientific cooperation partners from academia and industry.

Equal Opportunity

Applicants with disabilities will be given preference if equally qualified.
Female applicants are highly encouraged to apply, since women are under-represented in natural sciences and ZIB seeks to increase the proportion of women in this field.