Principal Scientist, Computational Chemistry

The role

You will influence discovery programs by generating structure-based insights and developing predictive models. You will partner with multidisciplinary teams to guide molecular design from hits to optimized leads.

What you will do

• Apply structure-based and ligand-based drug design methods to support projects from hit discovery through lead optimization.
• Collaborate with project team members in iterative structure-based drug design cycles.
• Present modeling insights to cross-functional project teams.
• Develop, refine, and maintain computational workflows on HPC Linux environments.
• Train and mentor colleagues on computational chemistry tools, cheminformatics standards, and workflow practices.

Required qualifications

• Ph.D. in Computational Chemistry or a related field
• 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
• 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
• Excellent scientific communication skills
• Proven effectiveness working within cross-functional, data-driven scientific teams

Nice to have

• working knowledge of other commercial and open-source computational chemistry platforms
• Strong programming skills with experience in building custom scripts or automated pipelines

Benefits

• competitive salary
• bonus
• ongoing stock awards
• 100% medical, dental, and vision premiums for you and your family
• funding up to 75% of in-network deductibles
• 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
• company-paid short-term disability coverage for up to 20 weeks
• wellness programs
• tuition reimbursement

About the company

Cogent Biosciences is a publicly traded biotechnology company focused on developing novel precision therapies to treat a broad range of patients with unmet medical needs.