Sr. Scientist, Protein Design

Moderna • Cambridge, MA

7d • $130,800 - $209,400

About The Position

Moderna is seeking a Senior Scientist to support the AI-enabled design of de novo antibodies, binder and antigen 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 and antigens. This position is strategically important to Moderna’s ability to initiate and execute multiple competitive binder programs in parallel. 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 Senior 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.
• Extensive post-PhD experience consistent with a Senior Scientist-level role in computational protein design.
• Hands-on experience in computational protein design, protein structural modeling, applied machine learning, or a closely related area.
• Strong publication and/or patent record demonstrating impact in protein design, structural biology, or applied machine learning.
• Experience with modern protein structure prediction and design tools, such as RFdiffusion, ProteinMPNN, AlphaFold-family methods, Rosetta, protein language models, or related generative approaches.
• Ability to work both independently and collaboratively in a fast-paced, cross-functional research environment.
• Strong critical-thinking, troubleshooting, and problem-solving skills.

Nice To Haves

• Experience scaling workflows on HPC and/or cloud (distributed compute, workflow orchestration, containerization).
• A desire to make an impact as part of a high-growth, transformational company that is Bold, Relentless, Curious, and Collaborative.

Responsibilities

• Apply AI-enabled protein design workflows to generate and prioritize de novo antibodies and binder modalities or partial de novo design of antigens for experimental testing.
• Use structure prediction, generative design, sequence design, docking, scoring, and developability analyses to create binder designs against diverse therapeutic targets.
• Help 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.
• Contribute to the 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.
• Contribute to cross-functional program and platform strategy discussions, helping shape Moderna’s long-term approach to AI-enabled protein design.

Benefits

• Competitive healthcare, 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 investments to help you plan for the future
• Location-specific perks and extras

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree