Senior Principal Scientist, Computational Chemistry

Cogent Biosciences • Boulder, CO

10d • Onsite

About The Position

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.

Requirements

• Ph.D. in Computational Chemistry or a related field, with 10 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.
• 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.

Nice To Haves

• Strong programming skills with experience in building custom scripts or automated pipelines, is a plus.

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.

Benefits

• 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.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree