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Senior Scientist (m/w/d) - AI/ML Antibody Modeling (TCRm & pHLA)
Full-Time | Emmendingen | Freiburg RegionWho we are
BioCopy is pioneering next-generation TCRm antibody therapeutics by unlocking the pHLA target space. Our ValidaTe platform uniquely integrates high-throughput wet-lab screening, structural insights, and AI to rapidly identify, validate, and optimize highly specific antibody candidates.Key responsibilities
Antibody & Protein Modeling
- Develop and apply deep learning and generative AI methods for antibody sequence and structure design.
- Build and refine protein language model-based pipelines for binding prediction, specificity optimization, and in silico affinity maturation.
- Implement structure-based and sequence-based tools for antibody-pHLA modeling and co-optimization.
- Design, train, and validate ML models using BioCopy’s internal datasets (e.g., peptide array binding data, ValidaTe outputs, structural features, PLM embeddings).
- Integrate geometric DL, transformer architectures, and multimodal models into antibody engineering workflows.
- Establish best practices for data preprocessing, model evaluation, and reproducible research.
- Work closely with antibody engineers, pHLA biology experts, and software engineers to co-design molecules and translate model predictions into wet-lab experiments.
- Contribute to BioCopy’s AI roadmap and help build scalable, maintainable computational infrastructure.
- Present results clearly to internal teams and leadership
Who You Are
- Hold a PhD in computational biology, structural biology, machine learning, bioinformatics, or a related field.
- Have strong experience with deep learning for proteins, such as:
- Protein language models (transformers)
- Geometric deep learning (GNNs, equivariant networks)
- Generative models (diffusion, VAEs)
- Are proficient in Python and frameworks like PyTorch, JAX, or TensorFlow.
- Have experience with antibody modeling, protein structure prediction, or immunology (a strong plus).
- Enjoy working in a fast-paced, highly collaborative biotech environment.
- Are motivated by scientific impact and want to help shape a young and ambitious AI program from the ground up.
What We Offer
- Unlimited employment and 30 days leave
- Flexible work hours, work-life balance
- Opportunity to build BioCopy’s AI/ML capabilities at a pivotal stage of growth.
- Close integration with wet-lab teams and real experimental feedback loops.
- Work on cutting-edge problems in TCRm design and pHLA targeting.
- A collaborative, low-bureaucracy environment where your ideas directly shape strategy.
- Competitive compensation package
- Modern office & lab environment in the Freiburg region with flexible working options.
To Apply:
Please submit your application (max. 10Mb) via email stating your earliest starting date and job Reference: JOB VACANCY P031.
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JOB VACANCY P031
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