Principal Scientist, Computational Chemistry

Biogen•Cambridge, MA

1d•$141,000 - $188,000

About The Position

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.

Requirements

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.

Nice To Haves

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.

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.

Benefits

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