Principal Scientist, Computational Chemistry

About the Role

New drugs are discovered through creative design and pioneering medicinal chemistry. In this role, you will leverage your modeling skills and knowledge of computational chemistry to support the design and prioritization of new small molecules aimed to treat neurological and rare diseases. You will be expected to work in a team environment and to effectively communicate with co-workers from a variety of disciplines and scientific backgrounds.

Key Responsibilities

• Serve as the primary computational chemistry contact for project teams, delivering design hypotheses and guiding medicinal chemistry optimization.
• Apply advanced structure based methods, including binding site analysis, pose prediction, and structure guided SAR development, to influence and prioritize compound design.
• Design, run, and interpret Free Energy Perturbation (FEP) calculations to predict potency and inform structure activity relationships.
• Employ molecular dynamics simulations, including enhanced sampling approaches to explore binding modes and protein conformational landscapes.
• Integrate data from cryo EM, X ray, and NMR structures to refine modeling and hypothesis generation.
• Use docking, ligand based methods, machine learning, QSAR modeling, and data analytics to support campaigns across multiple targets.
• Communicate complex computational results clearly and effectively to multidisciplinary audiences.
• Contribute to scientific excellence through publications, presentations, and evaluation of emerging computational technologies.

Who You Are

The successful candidate will be a creative and highly motivated scientist with demonstrated expertise in the field of computational chemistry and cheminformatics. You will be expected to stay current with the chemical literature and apply the latest advances in computational methods to address drug discovery project challenges. As a key contributor to small molecule discovery projects, thinking independently to solve complex problems is an important aspect of this position.

Required Skills

• Ph.D. in computational chemistry, cheminformatics, or related computational science discipline.
• 5+ years of pharma or biotech experience applying computational methods to small molecule drug discovery.
• Deep expertise in structure based drug design, including protein-ligand modeling and structure guided hypothesis generation.
• Hands-on experience with FEP workflows (e.g., setup, sampling, convergence assessment, interpretation).
• Proficiency in molecular dynamics, with experience using enhanced sampling techniques to probe binding mechanisms or conformational states.
• Demonstrated impact using docking, ligand based modeling, virtual screening, QM methods, and machine learning approaches.
• Track record of publications, and/or scientific presentations.
• Should be able to work in a multidisciplinary team.
• Excellent oral and written communication skills.

Preferred Skills

• Experience supporting medicinal chemistry optimization campaigns in understanding SAR and building hypotheses.
• Expertise with modern CADD software suites (e.g., Schrödinger, MOE, OpenEye) and proficiency in at least one scripting language (Python, Shell, R, or similar).
• Experience building predictive models using statistical or machine learning techniques, with strong knowledge of molecular descriptors and model validation.
• Ability to create automated workflows and pipelines for simulations, data analysis, or structure based modeling.
• Familiarity with integrating structural, biochemical, and ADME datasets to strengthen computational design strategies.

Job Level: Management

Additional Information

The base compensation range for this role is: $141,000.00-$188,000.00

Base salary offered is determined through an analytical approach utilizing a combination of factors including, but not limited to, relevant skills & experience, job location, and internal equity.

Regular employees are eligible to receive both short term and long-term incentives, including cash bonus and equity incentive opportunities, designed to reward recent achievements and recognize your future potential based on individual, business unit and company performance.

In addition to compensation, Biogen offers a full and highly competitive range of benefits designed to support our employees' and their families physical, financial, emotional, and social well-being; including, but not limited to:

• Medical, Dental, Vision, & Life insurances
• Fitness & Wellness programs including a fitness reimbursement
• Short- and Long-Term Disability insurance
• A minimum of 15 days of paid vacation and an additional end-of-year shutdown time off (Dec 26-Dec 31)
• Up to 12 company paid holidays + 3 paid days off for Personal Significance
• 80 hours of sick time per calendar year
• Paid Maternity and Parental Leave benefit
• 401(k) program participation with company matched contributions
• Employee stock purchase plan
• Tuition reimbursement of up to $10,000 per calendar year
• Employee Resource Groups participation

Why Biogen?

We are a global team with a commitment to excellence, and a pioneering spirit. As a mid-sized biotechnology company, we provide the stability and resources of a well-established business while fostering an environment where individual contributions make a significant impact. Our team encompasses some of the most talented and passionate achievers who have unparalleled opportunities for learning, growth, and expanding their skills. Above all, we work together to deliver life-changing medicines, with every role playing a vital part in our mission. Caring Deeply. Achieving Excellence. Changing Lives.

At Biogen, we are committed to building on our culture of inclusion and belonging that reflects the communities where we operate and the patients we serve. We know that diverse backgrounds, cultures, and perspectives make us a stronger and more innovative company, and we are focused on building teams where every employee feels empowered and inspired. Read on to learn more about our DE&I efforts.

All qualified applicants will receive consideration for employment without regard to sex, gender identity or expression, sexual orientation, marital status, race, color, national origin, ancestry, ethnicity, religion, age, veteran status, disability, genetic information or any other basis protected by federal, state or local law. Biogen is an E-Verify Employer in the United States.

Client-provided location(s): Cambridge, MA

Job ID: Biogen-REQ22962

Employment Type: FULL_TIME

Posted: 2026-04-01T23:54:10