Senior Scientist - Computational Protein Design

Amgen Inc. (IR); South San Francisco (CA); On-site; USD 146,000 - 198,000; Full time

Benefits offered by this job

Retirement plan

Medical, dental & vision coverage

Life and disability insurance

Flexible spending accounts

Discretionary annual bonus

Job summary

Amgen Inc. seeks a Senior Scientist in Computational Protein Design to develop and automate ML-driven design workflows for binder generation and to build scalable pipelines for large libraries of de novo proteins across multiple targets.

You will collaborate closely with experimental scientists and data teams to enable rapid validation and iteration, and you will contribute to shared tools and best practices within the protein design community.

Qualifications

• PhD/PharmD/MD with relevant post-doc in computational biology, structural biology, bioengineering, biophysics, computer science or related protein design field.
• Master’s degree with 3+ years of protein design experience in relevant setting.
• Bachelor’s degree with 5 years of protein design experience or equivalent.
• Experience in computational protein design, including design of minibinders and/or antibodies.

Responsibilities

• Develop and automate ML protein design workflows for binder generation.
• Build scalable pipelines for designing large libraries of de novo proteins across targets.
• Apply computational methods to support multiplexed screening and receptor discovery.
• Design and prioritize binders for targets and panels.
• Contribute to shared tools, workflows and best practices in protein design.
• Collaborate with experimental scientists and data teams for rapid validation and iteration.

Skills

Computational protein design

Python programming

AI/ML in protein design

Binder design (minibinders/antibodies)

High-throughput design

Protein structure knowledge

Education

PhD/MD/PharmD

Master’s degree + 3 years protein design

Bachelor’s degree + 5 years protein design

Tools

AlphaFold

ProteinMPNN

RFdiffusion

Python scripting

Cloud computing

HPC

Workflow orchestration tools

Job description

Senior Scientist - Computational Protein Design

Join Amgen’s Mission of Serving Patients At Amgen, if you feel like you’re part of something bigger, it’s because you are. Our shared mission—to serve patients living with serious illnesses—drives all that we do. Since 1980, we’ve helped pioneer the world of biotech in our fight against the world’s toughest diseases. With our focus on four therapeutic areas -Oncology, Inflammation, General Medicine, and Rare Disease- we reach millions of patients each year. Amgen is advancing a broad and deep pipeline of medicines to treat cancer, heart disease, inflammatory conditions, rare diseases, and obesity and obesity-related conditions. As a member of the Amgen team, you’ll help make a lasting impact on the lives of patients as we research, manufacture, and deliver innovative medicines to help people live longer, fuller happier lives. Our award-winning culture is collaborative, innovative, and science based. If you have a passion for challenges and the opportunities that lay within them, you’ll thrive as part of the Amgen team. Join us and transform the lives of patients while transforming your career.

What you will do

Let’s do this. Let’s change the world.

Key Responsibilities

• Develop and automate ML protein design workflows for binder generation
• Build scalable pipelines for designing large libraries of de novo proteins across multiple targets
• Apply computational methods to support multiplexed screening strategies and receptor discovery efforts
• Design and prioritize binders for individual targets and large target panels
• Contribute to shared tools, workflows, and best practices within the protein design community
• Collaborate closely with experimental scientists and data teams to enable rapid validation and iteration

What we expect of you

We are all different, yet we all use our unique contributions to serve patients. The Senior Scientist we seek is a Researcher with these qualifications.

Basic Qualifications

• Doctorate degree PhD OR PharmD OR MD [and relevant post-doc experience in Computational Biology, Structural Biology, Bioengineering, Biophysics, Computer Science, or related discipline with a focus on protein design] OR Master’s degree and 3 years of protein design experience OR Bachelor’s degree and 5 years of protein design experience

Preferred Qualifications

• Ph.D. with postdoc in Computational Biology, Structural Biology, Bioengineering, Biophysics, Computer Science, or related discipline with a focus on protein design.
• Demonstrated experience in computational protein design, including the design of binders such as minibinders and/or antibodies.
• Experience developing automated and scalable computational pipelines for protein design or structural modeling, ideally in high-throughput environments.
• Familiarity with modern AI/ML-driven protein design and structure prediction tools (e.g., AlphaFold, ProteinMPNN, RFdiffusion, or similar frameworks).
• Strong programming skills in Python and/or other scripting languages, with experience building maintainable workflows and automation for large-scale computational experiments.
• Experience working with large protein libraries or multiplexed design strategies, including design filtering, ranking, and diversity optimization.
• Knowledge of protein structure–function relationships, epitope targeting strategies, and protein–protein interaction design principles.
• Experience integrating computational design outputs with experimental validation workflows, including library generation, screening, or directed evolution approaches.
• Familiarity with cloud computing, high-performance computing (HPC), and workflow orchestration tools.
• Experience collaborating in cross-functional teams spanning computational scientists, experimental biologists, and data scientists.
• Strong communication skills and ability to contribute to a collaborative protein design community, including sharing tools, best practices, and design insights.

What you can expect from us

As we work to develop treatments that take care of others, we also work to care for your professional and personal growth and well-being. From our competitive benefits to our collaborative culture, we’ll support your journey every step of the way.

• A comprehensive employee benefits package, including a Retirement and Savings Plan with generous company contributions, group medical, dental and vision coverage, life and disability insurance, and flexible spending accounts
• A discretionary annual bonus program, or for field sales representatives, a sales-based incentive plan
• Stock-based long-term incentives
• Award-winning time-off plans
• Flexible work models where possible. Refer to the Work Location Type in the job posting to see if this applies.

Application deadline Amgen does not have an application deadline for this position; we will continue accepting applications until we receive a sufficient number or select a candidate for the position.

Sponsorship

Sponsorship for this role is not guaranteed. As an organization dedicated to improving the quality of life for people around the world, Amgen fosters an inclusive environment of diverse, ethical, committed and highly accomplished people who respect each other and live the Amgen values to continue advancing science to serve patients. Together, we compete in the fight against serious disease.

Amgen is an Equal Opportunity employer and will consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or any other basis protected by applicable law.

We will ensure that individuals with disabilities are provided reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. Please contact us to request accommodation.

Amgen is an Equal Opportunity employer and will consider you without regard to your race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, or disability status. Amgen will consider for employment qualified applicants with criminal histories in a manner consistent with the San Francisco Fair Chance Ordinance.

Salary Range

Salary Range 146,404.00USD -198,076.00 USD

The expected annual salary range for this role in the U.S. (excluding Puerto Rico) is posted.

Amgen is committed to unlocking the potential of biology for patients suffering from serious illnesses by discovering, developing, manufacturing and delivering innovative human therapeutics. This approach begins by using tools like advanced human genetics to unravel the complexities of disease and understand the fundamentals of human biology. Amgen focuses on areas of high unmet medical need and leverages its biologics manufacturing expertise to strive for solutions that improve health outcomes and dramatically improve people's lives. A biotechnology pioneer since 1980, Amgen has grown to be one of the world's leading independent biotechnology companies, has reached millions of patients around the world and is developing a pipeline of medicines with breakaway potential.

For more information, visit www.amgen.com and follow us on www.twitter.com/amgen