Senior Scientist - Computational Protein Design

Amgen • South San Francisco, CA

2d

About The Position

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. 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.

Requirements

• 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]
• Master’s degree and 3 years of protein design experience
• Bachelor’s degree and 5 years of protein design experience

Nice To Haves

• 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.

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

Benefits

• 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

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree