AI Tech Lead: Small Molecules

About Apheris

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. We host the industry’s largest federated data networks for drug discovery AI, spanning co-folding, ADMET, and antibody developability.

Across these networks, models are trained on proprietary industry datasets to achieve higher performance and broader applicability while keeping data control and IP protected. We deliver these superior models through drug discovery applications that enable teams to run them at scale, further customize them, and integrate them into existing R&D workflows.

• AI Structural Biology (AISB) Network: Pharmaceutical companies collaborate in the field of co-folding, structure-based binding affinity predictions and antibody design.
• ADMET Network: Pharmaceutical and biotech companies collaborate to improve small-molecule property prediction and expand to further drug modalities.
• Antibody Developability Network: Pharma partners collaborate to federate historical and purpose-built antibody developability datasets for secure ML training, without data leaving each partner’s environment.

About the role

We are looking for a technical lead to own delivery of our AI Structural Biology model programs.

This is a hands-on leadership role at the intersection of foundation models, structural biology, and federated learning. You will turn ambitious scientific goals into reliable model systems that can be evaluated, released, and used in real drug discovery workflows.

You will set technical direction, drive execution, challenge modeling decisions, and turn ambiguity into executable plans, while managing risks and dependencies, mentoring senior engineers and ML scientists, and getting into technical depth when needed.

We are looking for someone who has led demanding ML delivery before and knows how to move from research-led or open-source prototypes to robust model systems.

What you will do

• Lead the teams building and delivering federated co-folding models, staying hands-on across modeling, architecture, evaluation, and engineering execution.
• Build and implement ML applications in structural biology, particularly around fine-tuning and extending foundational models like OpenFold, Boltz-2 and ESMFold.Own delivery of these against committed milestones and ensure high-quality model releases ship on time.
• Translate ambiguous scientific and technical goals into clear plans, priorities, workstreams, and decisions.Guide evaluation decisions and build on them to deliver results packages to external stakeholders.
• Surface risks, blockers, bugs, timeline changes, and technical trade-offs early, with clear recommendations.
• Align consortium members on objectives, evaluation criteria, data requirements, timelines, and delivery expectations.
• Work with product, engineering, research, and leadership to ensure application requirements shape the model roadmap.

What we expect from you

You should apply if:

• You have a PhD, MSc, or equivalent experience in a relevant field, plus 5+ years applying ML to complex scientific or biological problems, ideally in structural biology, protein modeling, co-folding, or binding prediction.
• You have hands-on experience with modern ML systems in Python and PyTorch, and have worked with or extended large-scale models such as OpenFold, AlphaFold, Boltz, ESM, or similar.
• You have MLOps or ML infrastructure experience, particularly with Kubernetes-based training, evaluation, or deployment workflows.
• You can define success criteria,validate model quality, and ensure ML releases are robust enough for real-world use.
• You have led delivery of complex ML projects, including setting technical direction, managing risks and dependencies, and driving teams toward high-quality releases.
• You are comfortable operating as a player-coach: mentoring engineers and ML scientists while contributing directly to modeling, experimentation, or architecture when needed.
• You can work effectively with product, research, leadership, customers, and scientific stakeholders to turn ambiguous requirements into clear technical plans.

Bonus points if:

• You have experience with federated learning, privacy-preserving ML, distributed training, or other multi-party training environments.
• You have experience with Go or other systems programming languages.
• You have worked on production-grade model delivery in regulated, enterprise, pharmaceutical, biotech, or other high-trust environments.
• You have a publication record in top-tier ML, computational biology, or structural biology venues such as NeurIPS, ICML, ICLR, ISMB, RECOMB, or similar.

What we offer you

• Industry-competitive compensation, including early-stage virtual share options
• Remote-first working – work where you work best
• Wellbeing budget, mental health support, work-from-home budget, co-working stipend, and learning budget
• Generous holiday allowance
• Office Days at our Berlin HQ or a different European location (3x per year)
• A high-calibre, execution-focused team with experience from leading organizations