Principal Scientist, Protein Design

The Role

Moderna is seeking a Principal Scientist to support the AI‑enabled design of de novo antibodies and binder modalities across diverse discovery programs. This is a hands‑on, highly technical role for an experienced protein designer who can build and operationalize agentic AI design frameworks and translate modern generative methods into validated binders. The role is strategically important to Moderna’s ability to initiate and execute multiple competitive binder programs in parallel and offers a rare opportunity to invent how AI‑designed binders function in vivo as part of mRNA therapeutics.

The Principal Scientist will work closely with and report to the Senior Director, Computational Design and In Vitro Selection, and will also work closely with the VP, Protein Design, as well as other members of Research, to advance novel candidates to the clinic and establish Moderna as a leader in antibody and de novo binder design for in vivo delivery.

• Executing design strategy as the primary AI protein designer for de novo antibody and binder modalities.
• Build and maintain AI protein design frameworks for binders, including application of generative methods, model training/inference workflows, automated design creation, scoring, filtering, and prioritization.
• Partner closely with experimental teams to interpret screening/selection/biophysical data and drive iterative design cycles that improve affinity, specificity, stability, expression, and develop ability.
• Define and implement benchmarking and validation standards for new methods, ensuring computational efforts are program‑ready rather than exploratory.
• Develop and iteratively optimize multi‑agent systems to accelerate and enhance AI computational design and to create closed‑loop automated design‑and‑wet‑lab‑test systems.
• Mentor and technically guide other computational designers and data scientists, elevating overall AI design quality and rigor across the organization.
• Contribute to cross‑functional program and platform strategy discussions, helping shape Moderna’s long‑term approach to AI‑enabled protein design.

• PhD in Biophysics, Biochemistry, Structural Biology, Computational Biology, or a related field with 5+ years of experience.
• Extensive post‑PhD experience consistent with a Principal Scientist‑level role in computational protein design.
• Strong publication and/or patent record demonstrating impact in protein design, structural biology, or applied machine learning.
• Strong hands‑on coding ability with demonstrated experience building production‑grade scientific software and pipelines (Python required; additional languages a plus).
• Demonstrated experience with building and optimizing agentic AI systems for computational design.
• Practical experience developing and/or deploying ML models for proteins.
• Ability to mentor, review, and elevate the work of other designers.

• Experience scaling workflows on HPC and/or cloud (distributed compute, workflow orchestration, containerization).
• Proven track record of designing antibody‑based biologics.
• A desire to make an impact as part of a high‑growth, transformational company.

The salary range for this role is $ – $. An individual’s position within the salary range will be based on several factors including, but not limited to, specific competencies, relevant education, qualifications, certifications, experience, skills, performance, and business or organizational needs. The successful candidate may be eligible for an annual discretionary bonus, other incentive compensation, or equity award, subject to company plan eligibility criteria and individual performance.

• Best‑in‑class healthcare coverage, plus voluntary benefit programs to support your unique needs.
• A holistic approach to well‑being, with access to fitness, mindfulness, and mental health support.
• Family planning benefits, including fertility, adoption, and surrogacy support.
• Generous paid time off, including vacation, volunteer days, sabbatical, global recharge days, and a discretionary year‑end shutdown.
• Savings and…