Sr. Data Scientist – Computational Drug Discovery

What you will do

Let’s do this. Let’s change the world. We are seeking a Data Scientist with strong expertise in molecular simulation and machine learning to join the AI & Data for Engineered Biologics team within Amgen’s Large Molecule Discovery (LMD) organization. In this vital role you will advance Amgen’s discovery programs through the development and application of molecular simulation, structural modeling, and machine learning approaches for large-molecule therapeutic design. You will work at the interface of physics-based modeling and data-driven prediction to generate mechanistic insight, guide experimental design, and enable candidate optimization across biologics discovery workflows.

The successful candidate will work in a highly collaborative, multidisciplinary environment, partnering with structural biology, protein engineering, computational and data sciences, and experimental discovery teams to impact programs from target and hit validation through lead optimization and candidate selection.

Key Responsibilities

• Design and execute molecular dynamics simulations, including enhanced-sampling and kinetics-focused approaches, to study protein structure, conformational dynamics, binding mechanisms, and biomolecular interactions relevant to large-molecule therapeutic discovery
• Develop and apply machine learning models leveraging molecular simulation, sequence, structural, repertoire, and experimental data to predict molecular properties, prioritize designs, and generate testable hypotheses
• Build integrated modeling frameworks that combine multi-modal biological data to enable therapeutic design and data-driven decision-making
• Incorporate physics-based insights from molecular simulations (e.g., conformational ensembles, dynamics) into machine learning models to improve interpretability and predictive accuracy
• Develop and scale robust computational workflows, reusable pipelines, and modeling platforms to ensure reproducibility and efficiency across discovery programs
• Mentor and provide technical guidance to junior data scientists and computational scientists, supporting best practices in modeling and analysis
• Collaborate cross-functionally with structural biology, protein engineering, and experimental teams to define computational strategies, prioritize experiments, and translate insights into actionable outcomes
• Evaluate and implement emerging methods in machine learning, generative modeling, and molecular simulation to enhance the Amgen’s computational discovery toolkit
• Communicate scientific findings and recommendations clearly through presentations, technical documentation, and publications

What we expect of you

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

Basic Qualifications

PhD in Computational Biology, Computational Chemistry, Theoretical Chemistry, Biophysics, or a related field

Or

Master’s degree and 3 years of directly related experience

Or

Bachelor’s degree and 5 years of directly related experience

Preferred Qualifications

• Postdoctoral or equivalent research experience in molecular simulation, computational biophysics, or AI-accelerated drug discovery
• Deep expertise in molecular dynamics simulations of biomolecular systems, including enhanced sampling, rare-event methods, free-energy or kinetics analysis, and interpretation of conformational ensembles
• Strong programming skills in Python and experience with modern ML frameworks (e.g., PyTorch) and molecular simulation / modeling software such as GROMACS, OpenMM, Amber, NAMD, or related tools
• Experience deriving machine learning features or representations from molecular simulation trajectories and integrating them with sequence, structural, and experimental data
• Proven ability to apply machine learning methods such as supervised learning, deep learning, generative modeling, active learning, or optimization methods to molecular design or drug discovery problems
• Experience working with large-scale datasets and high-performance computing environments, including cloud-based platforms (e.g., AWS)
• Experience integrating molecular modeling and machine learning with structural and biophysical data, including cryo-EM, X-ray, HDX, or related experimental readouts
• Familiarity with software engineering best practices for reproducible scientific computing, including version control (git), testing, containerization (Docker), and workflow orchestration tools
• Experience supporting biologics, protein engineering, or large-molecule therapeutic discovery is strongly preferred
• Strong scientific communication skills, with a demonstrated publication record
• Demonstrated ability to influence cross-functional teams by translating computational results into clear, actionable scientific recommendations

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.

Amgen is proud to have been recognized as one of LinkedIn Top 25 Companies in Canada for career growth. Click for more details.

The salary of this position in Canada is $117,808 - $159,388.

In addition to the base salary, Amgen offers competitive and comprehensive Total Rewards Plans that are aligned with local industry standards.

Salary Range