Principal Scientist, Computational Chemistry

Cogent Biosciences, Inc.; Boulder (CO); On-site; USD 165,000 - 190,000; Full time

Benefits offered by this job

Stock awards

Full benefits

Retirement match

Parental leave

Paid time off

Disability coverage

Wellness programs

Tuition reimbursement

Job summary

Cogent Biosciences, Inc. is seeking a Principal Scientist in Computational Chemistry for its Boulder, Colorado—on‑site—R&D facility. You will lead structure‑based and ligand‑based design efforts to translate hits into optimized lead compounds, guiding SAR through data‑driven strategies and cross‑functional collaboration.

You will develop scalable HPC workflows, mentor scientists, and communicate complex modeling results clearly. A Ph.D.

Qualifications

• Ph.D. in Computational Chemistry or related field with 3+ years of industrial experience.
• Expertise in structure-based design, docking, virtual screening, pharmacophore modeling, and lead optimization.
• Strong Linux/UNIX, HPC workflow and scripting skills; experience with MOE and cheminformatics tools.

Responsibilities

• Apply structure-based and ligand-based design methods to support hit discovery through lead optimization.
• Collaborate with teams to generate hypotheses and triage hits for SAR exploration.
• Present modeling insights clearly to cross-functional project teams.
• Develop and maintain scalable computational workflows on HPC Linux environments.
• Train and mentor colleagues in computational chemistry tools and workflows.

Skills

Structure-based design

Docking

Virtual screening

Pharmacophore modeling

MOE modeling

Cheminformatics tools

Programming (scripting)

Linux/UNIX

HPC / cluster computing

Education

Ph.D. in Computational Chemistry or related field

Tools

MOE

Spotfire

SLURM

LSF

PBS/Torque

Job description

Principal Scientist, Computational Chemistry

Who We Are:

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. Cogent’s lead program, bezuclastinib, is designed to selectively and potently inhibit exon 17 mutations found within the KIT receptor tyrosine kinase, including KIT D816V. KIT D816V is responsible for driving a rare and serious condition called Systemic Mastocytosis, and exon 17 mutations are also found in patients with gastrointestinal stromal tumors (GIST), a type of cancer with strong dependence on oncogenic KIT signaling. Bezuclastinib has exhibited promising initial data across all three trials: APEX in AdvSM, SUMMIT in NonAdvSM, and PEAK in GIST, including an encouraging safety profile across 600+ patients in single-agent and combination dosing.

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

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

• competitive salary, bonus, and ongoing stock awards


• We cover 100% of medical, dental, and vision premiums for you and your family


• Help reduce out-of-pocket costs by 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


• Additional perks like wellness programs, tuition reimbursement, and inclusive family‑forming support

We are proud to be an Equal Opportunity Employer. Our goal is to have a diverse workforce. We do not discriminate on the basis of race, age, color, religion, national origin, gender, sexual orientation, gender identity or expression, veteran status or disability, or any other status protected under federal, state, or local law. All employment is decided on the basis of qualifications, merit, and business need.