Principal Scientist, Protein Design

Moderna • Cambridge, MA

2d • Onsite

About The Position

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. This position is strategically important to Moderna’s ability to initiate and execute multiple competitive binder programs in parallel. As a Principal Scientist, you will also mentor other designers and act as a visible scientific agentic AI design resource across the organization. This role offers a rare opportunity to invent how AI-designed binders function in vivo as part of mRNA therapeutics: as stand-alone biologics, targeting modules, or components of next-generation multi-protein systems. 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.

Requirements

• 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.

Nice To Haves

• 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 that is Bold, Relentless, Curious, and Collaborative.

Responsibilities

• 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 developability.
• 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.

Benefits

• 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 investment opportunities to help you plan for the future
• Location-specific perks and extras

What This Job Offers

• Job Type: Full-time
• Career Level: Principal
• Education Level: Ph.D. or professional degree
• Number of Employees: 1,001-5,000 employees