Sr. Scientist, Protein Design

RXinsider LTD.; 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

The Role

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.

Here’s What You’ll Do

• 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.

Here’s What You’ll Need (Basic 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.
• 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.

Here’s What You’ll Bring to the Table (Preferred Qualifications)

• 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.

Pay & Benefits

At Moderna, we believe that when you feel your best, you can do your best work.

That’s why our benefits and well‑being resources are designed to support you—at work, at home, and everywhere in between.

• 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

The salary range for this role is $130,800.00 - $209,400.00. This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. 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.

About Moderna

Since our founding in 2010, we have aspired to build the leading mRNA technology platform, the infrastructure to reimagine how medicines are created and delivered, and a world‑class team. We believe in giving our people a platform to change medicine and an opportunity to change the world.

By living our mission, values, and mindsets every day, our people are the driving force behind our scientific progress and our culture. Together, we are creating a culture of belonging and building an organization that cares deeply for our patients, our employees, the environment, and our communities.

We are proud to have been recognized as a Science Magazine Top Biopharma Employer, a Fast Company Best Workplace for Innovators, and a Great Place to Work in the U.S.

If you want to make a difference and join a team that is changing the future of medicine, we invite you to visit modernatx.com/careers to learn more about our current opportunities.

Equal Opportunities

Moderna is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry or citizenship, ethnicity, disability, military or protected veteran status, genetic information, sexual orientation, marital or familial status, or any other personal characteristic protected under applicable law. Moderna is a place where everyone can grow.

Moderna is an E-Verify Employer in the United States. We consider qualified applicants regardless of criminal histories, consistent with legal requirements.

Accommodations

We’re focused on attracting, retaining, developing, and advancing our employees. By cultivating a workplace that values diverse experiences, backgrounds, and ideas, we create an environment where every employee can contribute their best.

Moderna is committed to offering reasonable accommodations to qualified job applicants with disabilities. Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should contact the Accommodations team at [e-mail].

Export Control Notice

This position may involve access to technology or data that is subject to U.S. export control laws, including the Export Administration Regulations (EAR). As such, employment is contingent upon the applicant’s ability to access export‑controlled information in accordance with U.S. law. Due to the nature of the work and regulatory requirements, only individuals who qualify as U.S. persons (citizens, permanent residents, asylees, or refugees) are eligible for this position. For this role Moderna is unable to sponsor non‑U.S. persons to apply for an export control license.