Sr. Data Scientist – Computational Drug Discovery

Amgen; Burnaby; On-site; CAD 118,000 - 159,000; Full time

Job summary

Amgen seeks a Sr. Data Scientist in Canada to advance computational drug discovery through molecular simulation, ML, and integrated modeling across large‑molecule programs.

You will collaborate with biology, chemistry, and engineering teams to design experiments, interpret results, and guide optimization of biologics candidates. The role emphasizes developing scalable workflows, reproducible analyses, and impactful scientific communications to support candidate selection and translational

Qualifications

• PhD in Computational Biology, Computational Chemistry, Theoretical Chemistry, Biophysics, or related field
• Master’s degree and 3 years of directly related experience
• Bachelor’s degree and 5 years of directly related experience
• 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
• Strong programming skills in Python and 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
• Experience working with large‑scale datasets and high‑performance computing environments, including cloud‑based platforms (e.g., AWS)
• 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

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 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

Skills

Python

PyTorch

Molecular dynamics

ML for drug design

HPC

AWS

Education

PhD in Computational Biology/Computational Chemistry/Biophysics

Master’s degree + 3 years related experience

Bachelor’s degree + 5 years related experience

Tools

GROMACS

OpenMM

Amber

NAMD

Docker

Git

Job description

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.

Sr. Data Scientist – Computational Drug Discovery

What You Will Do

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
• Master’s degree and 3 years of directly related experience
• 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

What You Can Expect Of 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.

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

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.

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.