Senior Scientist - Computational Protein Design

BioSpace; South San Francisco (CA); Hybrid; USD 140,000 - 190,000; Full time

Job summary

Amgen is seeking a Senior Scientist in Computational Protein Design to develop and deploy automated pipelines for binder design across multiple targets. You will accelerate discovery by generating diverse libraries and integrating computational design with experimental validation.

The role emphasizes collaboration with computational, experimental, and data science teams and requires strong Python and modern AI/ML tool experience. Flexible work models are available where possible.

Qualifications

• PhD/MD/PharmD or equivalent with focus on protein design.
• Experience in computational protein design and library design.
• Strong programming and scripting skills in Python or similar languages.

Responsibilities

• Develop and automate ML protein design workflows for binder generation.
• Build scalable pipelines for de novo protein design across multiple targets.
• Apply computational methods to support multiplexed screening and receptor discovery.
• Design and prioritize binders for targets and large panels.
• Collaborate with experimental scientists and data teams to enable rapid validation.

Skills

ML protein design

Python

Protein design workflows

Automation pipelines

Education

Doctorate (PhD) or equivalent

Postdoc in relevant field

Tools

Cloud computing

RFdiffusion/AlphaFold

High-performance computing

Bioinformatics tooling

Job description

Join Amgens Mission of Serving Patients

At Amgen, if you feel like youre part of something bigger, its because you are. Our shared missionto serve patients living with serious illnessesdrives all that we do.

Since 1980, weve helped pioneer the world of biotech in our fight against the worlds 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, youll 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, youll thrive as part of the Amgen team. Join us and transform the lives of patients while transforming your career.

Senior Scientist - Computational Protein Design

What You Will Do

Lets do this. Lets change the world. In this vital role you will develop and deploy automated computational pipelines for large-scale binder design, supporting the creation of diverse design candidates and libraries across multiple targets. Your work will directly enable discovery efforts by accelerating the generation of molecules used to probe novel biology and deliver new biological insights.

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 Masters degree and 3 years of protein design experience

OR Bachelors 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 structurefunction relationships, epitope targeting strategies, and proteinprotein 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, well support your journey every step of the way.

The expected annual salary range for this role in the U.S. (excluding Puerto Rico) is posted. Actual salary will vary based on several factors including but not limited to, relevant skills, experience, and qualifications.

In Addition To The Base Salary, Amgen Offers a Total Rewards Plan, Based On Eligibility, Comprising Of Health And Welfare Plans For Staff And Eligible Dependents, Financial Plans With Opportunities To Save Towards Retirement Or Other Goals, Work/life Balance, And Career Development Opportunities That May Include

• 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.

In any materials you submit, you may redact or remove age-identifying information such as age, date of birth, or dates of school attendance or graduation. You will not be penalized for redacting or removing this information.

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, and disability status.