Scientist, Protein Design

Initial Therapeutics, Inc.; Cambridge (MA); On-site; USD 109,000 - 175,000; Full time

Benefits offered by this job

Healthcare benefits

Well-being resources

Family planning benefits

Generous paid time off

Financial planning and retirement

Job summary

Moderna is seeking a Scientist to contribute to AI-enabled design of de novo antibodies and binder modalities across discovery programs. You will apply modern generative methods and structure-based design tools to create and score designs for experimental validation in a fast-paced, collaborative setting in Cambridge, MA.

The role emphasizes strong coding and protein-design skills, with opportunities to prototype agentic AI workflows and advance mRNA therapeutics through cross-functional

Qualifications

• PhD in Biophysics, Biochemistry, Structural Biology, Computational Biology, Computer Science, or related field.
• Hands-on experience in computational protein design, protein structural modeling, ML, or related area.
• Strong Python coding skills and experience building reproducible workflows.
• Experience with modern protein structure prediction and design tools (RFdiffusion, ProteinMPNN, AlphaFold, Rosetta).

Responsibilities

• Apply AI-enabled protein design workflows to generate and prioritize de novo antibodies and binder modalities for experimental testing.
• Use structure prediction, generative design, docking, scoring, and developability analyses to design binders against targets.
• Build and improve Python-based workflows for model inference, design generation, scoring, filtering, and visualization.
• Collaborate with experimental teams to interpret screening data and guide iterative design cycles.
• Contribute to benchmarking and validation of new computational methods for binder-design campaigns.
• Explore agentic AI design workflows linking target analysis, design generation, scoring, and experimental feedback.
• Develop understanding of targets through literature review and data analysis, communicating results with project teams.
• Stay updated on advances in generative protein design and antibody engineering.

Skills

Python coding

Computational design

Structure prediction

Team collaboration

Education

PhD in Biophysics/Biochemistry/Structural Biology/Computational Biology/CS

Tools

RFdiffusion

ProteinMPNN

AlphaFold-family

Rosetta

Job description

The Role

Moderna is seeking a talented, creative, and motivated Scientist to contribute to the AI-enabled design of de novo antibodies or other binder modalities and de novo design of antigens across discovery programs. This is a hands-on computational protein design role for a scientist who can apply modern generative methods, agentic AI workflows, and structure-based design tools to help create, score, and improve binders and antigens for experimental validation. The Scientist will be part of a highly collaborative, multidisciplinary team working to invent how AI-designed binders can function in vivo as part of mRNA therapeutics, including as stand-alone biologics, targeting modules, and components of next-generation multi-protein systems.

The Scientist will work closely with computational designers, data scientists, and experimental teams within Computational Design and In Vitro Selection and across Moderna Research to advance novel mRNA-delivered protein candidates. The ideal candidate will bring strong coding and protein-design skills, curiosity about new AI-enabled design approaches, and the ability to translate experimental feedback into improved designs. This is a unique opportunity to work in an innovative environment at the intersection of AI protein design, de novo binder discovery, and mRNA therapeutics.

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.
• Build, maintain, and improve Python-based workflows for model inference, automated design generation, scoring, filtering, and result visualization under the guidance of senior team members.
• Partner with experimental colleagues to interpret screening, selection, biophysical, and developability data, and use those data to guide iterative design cycles.
• Contribute to benchmarking and validation of new computational methods so that promising tools can be incorporated into binder-design campaigns.
• Explore and prototype agentic AI design workflows that connect target analysis, design generation, scoring, and experimental feedback.
• Develop biological and structural understanding of assigned targets through literature review, analysis of internal and external data, and discussion with project teams.
• Collaborate with cross-functional teammates to plan experiments, summarize design rationale, and communicate results in team meetings and written updates.
• Maintain awareness of advances in generative protein design, agentic AI systems, antibody engineering, and de novo binder discovery.
• Contribute scientifically and technically to multiple discovery efforts in parallel.

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

• PhD in Biophysics, Biochemistry, Structural Biology, Computational Biology, Computer Science, or a related field.
• Hands-on experience in computational protein design, protein structural modeling, applied machine learning, or a closely related area.
• Strong Python coding skills and experience building reproducible scientific analysis or design workflows in Linux-based environments.
• 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 analyze protein designs and experimental datasets, identify next design steps, and communicate conclusions clearly to multidisciplinary collaborators.
• Strong critical-thinking, troubleshooting, and problem-solving skills.
• Excellent written, presentation, and interpersonal communication skills.
• Ability to work both independently and collaboratively in a fast-paced, cross-functional research environment.

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

• Experience designing antibody-based biologics or de novo binders.
• Experience developing workflows for HPC or cloud environments, including distributed computing, workflow orchestration, or containerization.
• Experience benchmarking protein design methods, evaluating ML models, or contributing to closed-loop design-test-learn campaigns.
• Experience with agentic AI or LLM-enabled automation for scientific workflows.
• Familiarity with in vitro selection, display technologies, SPR, Octet, developability assessment, or related experimental approaches for binder characterization.
• Track record of publications, presentations, or patents in protein design, structural biology, antibody engineering, or applied machine learning.
• 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 $109,200.00 - $174,600.00. 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.

Our Working Model

As we build our company, we have always believed an in-person culture is critical to our success. Moderna champions the significant benefits of in-office collaboration by embracing a 70/30 work model. This 70% in-office structure helps to foster a culture rich in innovation, teamwork, and direct mentorship. Join us in shaping a world where every interaction is an opportunity to learn, contribute, and make a meaningful impact.

Moderna is a smoke-free, alcohol-free, and drug-free work environment.

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.Moderne is a place where everyone can grow. If you meet the Basic Qualifications for the role and you would be excited to contribute to our mission every day, please apply!

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.