Principal Scientist, Protein Design

Initial Therapeutics, Inc.; Cambridge (MA); On-site; USD 142,500 - 256,500; Full time

Benefits offered by this job

Best-in-class healthcare coverage

Generous paid time off

Family planning benefits

Job summary

Moderna is seeking a Principal Scientist located in Cambridge, MA, to facilitate AI-enabled protein design, focusing on antibodies and binder modalities. This hands-on role demands expertise in computational protein design and mentoring capabilities. The successful candidate will work closely with senior leadership and experimental teams to enhance protein affinity and stability, while contributing to strategic program discussions. Competitive salary range: $142,500.00 – $256,500.00, with excellent benefits including healthcare coverage and generous paid leave.

Qualifications

• 5+ years of post-PhD experience in computational protein design.
• Strong publication and/or patent record.
• Experience developing and deploying ML models for proteins.

Responsibilities

• Execute design strategy as the primary AI protein designer.
• Partner with experimental teams to drive design iterations.
• Mentor computational designers and data scientists.

Skills

Strong hands-on coding ability

Experience in computational protein design

Mentoring capabilities

Building and optimizing agentic AI systems

Education

PhD in Biophysics, Biochemistry, Structural Biology, or related field

Tools

Python

HPC/cloud experience

Job description

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.

Here’s What You’ll Do

• 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.

Here’s What You’ll Need (Basic Qualifications)

• 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.

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

• 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.

Pay & Benefits

The salary range for this role is $142,500.00 – $256,500.00. 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 investment opportunities to help you plan for the future.
• Location‑specific perks and extras.

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

Accommodations

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.