Senior Scientist, AI-Enabled Protein Design

Moderna; Cambridge (MA); On-site; USD 131,000 - 209,000; Full time

Benefits offered by this job

Healthcare

Well-being resources

Family planning benefits

Generous paid time off

Equity or incentive programs

Job summary

Moderna is seeking a Senior Scientist to lead AI-enabled design of de novo antibodies, binder and antigen modalities across discovery programs. This is a hands-on, highly technical role for an experienced protein designer who can operationalize agentic AI design frameworks and translate generative methods into validated binders and antigens.

The Senior Scientist will collaborate with senior leadership to advance novel candidates to the clinic, shaping Moderna’s position in antibody and de novo

Qualifications

• 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.

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.

Skills

AI-enabled protein design

Computational protein design

Structure prediction

Machine learning

Collaboration

Education

PhD in Biophysics/Biochemistry/Structural Biology/Computational Biology or related

Tools

RFdiffusion

ProteinMPNN

AlphaFold

Rosetta

Protein language models

Job description

Moderna is seeking a Senior Scientist to lead AI-enabled design of de novo antibodies, binder and antigen modalities across discovery programs. This is a hands-on, highly technical role for an experienced protein designer who can operationalize agentic AI design frameworks and translate generative methods into validated binders and antigens.

The Senior Scientist will collaborate with senior leadership to advance novel candidates to the clinic, shaping Moderna’s position in antibody and de novo