Cogent Biosciences

Research Investigator, Computational Chemistry

Boulder, Colorado, United States · Full-time

Sponsorship not specified$180k-$210kDetected 23 days ago

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About the role

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.
Develop, refine, and maintain robust computational workflows on HPC Linux environments, enabling scalable execution of large‑scale simulations.

Requirements

Ph.D. in Computational Chemistry or a related field, with 10 years of relevant industrial experience.
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).
Proven effectiveness working within cross‑functional, data‑driven scientific teams.
Expertise in structure‑based design, docking, virtual screening, pharmacophore modeling, and other computational approaches for lead optimization.
Strong programming skills with experience in building custom scripts or automated pipelines, is a plus.
A solid publication record and excellent scientific communication skills.

Nice to have

Expertise in MOE modeling software, with working knowledge of other commercial and open‑source computational chemistry platforms preferred.

Compensation

$ 180k - $210k USD
Exact compensation will vary based on skills, experience, and location.
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.
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

Benefits

At Cogent Biosciences, we offer a competitive salary, bonus, and ongoing stock awards, alongside a benefits package that se t s 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.
A dditional perks like wellness programs, tuition reimbursement, and inclusive family-forming support help you thrive at work and beyond.

Company info

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.
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.
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.
Our headquarters is located in the Greater Boston life sciences community, with an open, collaborative office environment designed to support teamwork and connection.
We are proud to be an

Equal opportunity

We are proud to be an Equal Opportunity Employer.
Our goal is to have a diverse workforce.
Equal Opportunity Employer.

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