Principal Scientist, Computational Chemistry

The Role

We are seeking an Experienced Computational Chemist who thrives at the intersection of molecular modeling, data-driven decision making, and innovative drug design. In this role, you will directly influence discovery programs by generating actionable structure-based insights, developing predictive models, and partnering with multidisciplinary teams to guide molecular design from hits to optimized leads. This is a full-time, on-site position based at our R&D facility in Boulder, Colorado.

Responsibilities

• Apply structure-based and ligand-based drug design methods-including docking, protein modeling, and a range of computational techniques-to support projects from hit discovery through lead optimization.
• Collaborate with project team members, engaging them in iterative structure-based drug design cycles to generate hypotheses, evaluate targets, triage hits, and guide SAR exploration.
• Present modeling insights clearly and effectively to cross-functional project teams, ensuring data is interpreted in the right context.
• Develop, refine, and maintain robust computational workflows on HPC Linux environments, enabling scalable execution of large-scale simulations.
• Train and mentor colleagues on computational chemistry tools, cheminformatics standards, data formats, and key workflow practices.

Qualifications

• Ph.D. in Computational Chemistry or a related field, with 3+ years of relevant industrial experience.
• Expertise in structure-based design, docking, virtual screening, pharmacophore modeling, and other computational approaches for lead optimization.
• Expertise in MOE modeling software, with working knowledge of other commercial and open-source computational chemistry platforms preferred.
• Strong hands-on experience with cheminformatics platforms and tools, including Spotfire.
• Strong programming skills with experience in building custom scripts or automated pipelines, is a plus.
• Proficiency in Linux/UNIX, shell scripting, and HPC frameworks (e.g., SLURM, LSF, PBS/Torque).
• Experience optimizing large computational workloads on cluster or cloud infrastructure.
• Familiarity with molecular representations and cheminformatics standards (SMILES, SDF, descriptors, fragment-based encodings).
• A solid publication record and excellent scientific communication skills.
• Proven effectiveness working within cross-functional, data-driven scientific teams.

Salary Range

$165k - 190k USD

Target Bonus: 15%

Exact compensation will vary based on skills, experience, and location.

Our Locations

Waltham, MA: Our headquarters is located in the Greater Boston life sciences community, with an open, collaborative office environment designed to support teamwork and connection. Employees benefit from convenient on-site amenities, including free on-site parking and gym facilities in the building.

Boulder, CO: Our Boulder location is home to Cogent's discovery research organization and a key scientific hub with strong leadership based on site. Situated in the greater Denver-Boulder biopharmaceutical corridor, this office plays a central role in advancing our discovery efforts and pipeline.

Our Offer To You

At Cogent Biosciences, we offer a competitive salary, bonus, and ongoing stock awards, alongside a benefits package that sets us apart. We cover 100% of medical, dental, and vision premiums for you and your family, and help reduce out-of-pocket costs by funding up to 75% of in-network deductibles.

Our benefits also include a 401(k) match with immediate vesting, generous paid time off, 12 weeks of fully paid parental leave, paid family and medical leave for all employees regardless of location, and company-paid short-term disability coverage for up to 20 weeks. Additional perks like wellness programs, tuition reimbursement, and inclusive family-forming support help you thrive at work and beyond.