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Senior Machine Learning Engineer (Structural Biology) - Federated AI for Drug Discovery

apheris • European Economic Area
Full Remote
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Build and deploy advanced ML models for protein structure prediction and drug discovery workflows. Focus on fine-tuning foundational models (e.g., OpenFold, Boltz-2) and designing scalable pipelines for cofolding, binding affinity, and antibody design. Requires deep expertise in ML production, MLOps, and structural biology applications.

Key Highlights
Focus on structural biology models (e.g., OpenFold, Boltz-2, ESMFold) for drug discovery.
Hands-on role with ownership of model development, deployment, and customer collaboration.
Federated AI infrastructure with governance and privacy controls for pharmaceutical data.
Key Responsibilities
Build and deploy ML models for protein structure prediction and drug discovery.
Design scalable data preprocessing, training, and evaluation workflows for structural biology tasks.
Collaborate with customers and academic partners to define data strategies and case studies.
Develop and maintain production-ready ML pipelines and models.
Technical Skills Required
Machine Learning (ML) Model Development Structural Biology Applications MLOps and Scalable Pipeline Design
Benefits & Perks
Industry-competitive compensation and early-stage virtual share options
Remote-first working with a work-from-home budget and co-working stipend
Wellbeing budget, mental health benefits, generous holiday allowance, and learning & development budget
Nice to Have
Experience in federated learning or privacy-preserving ML.
Publications in ML or biology journals/conferences.
Experience in a fast-paced startup environment.

Job Description

At Apheris, we are building the future of how AI is applied in pharmaceutical R&D. We enable leading pharmaceutical teams to discover and develop drugs faster through federated data networks for drug discovery AI, including co-folding, ADMET, and antibody developability.

About The Role

We are looking for a Senior ML Engineer to drive the technical execution for our structural biology models. This hands-on role focuses on advancing state-of-the-art foundational models for structural biology problems, working closely with leadership and customers.

You will:

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