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Computational Chemistry Software Developer Jobs in Colorado

Cymertek

HPC Software Architect

Aurora, CO · On-site

HPC Software Architect LOCATION Aurora, CO 80014 CLEARANCE TS/SCI Full Poly (Please note this ... Engineering, Computational Biology, Computational Chemistry, Information Technology, Systems ...

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Computational Chemistry Software Developer information

What is the difference between Computational Chemistry Software Developer vs Computational Chemist?

AspectComputational Chemistry Software DeveloperComputational Chemist
Required CredentialsBachelor's or Master's in Chemistry, Computer Science, or related fieldBachelor's or Master's in Chemistry, Chemical Engineering, or related field
Work EnvironmentSoftware development teams, research labs, tech companiesResearch labs, academic institutions, pharmaceutical companies
Employer & Industry UsageTech firms, software companies, scientific research organizationsPharmaceuticals, academia, chemical industries
Common Search & ComparisonYesYes

While both roles involve chemistry and computational skills, Computational Chemistry Software Developers focus on creating and maintaining software tools used by chemists, whereas Computational Chemists primarily conduct research and simulations to understand chemical phenomena. The roles often overlap in skills but differ in daily tasks and focus areas.

What is a computational chemistry software developer?

Computational Chemistry Software Developers are professionals who design, build, and maintain software tools used for modeling and simulating chemical systems. They combine expertise in chemistry, computer science, and mathematics to create programs that help researchers understand molecular structures, reactions, and properties. These developers work closely with scientists to implement algorithms, optimize code performance, and ensure software usability for various computational chemistry applications. Their work supports advancements in fields like drug discovery, materials science, and chemical engineering.

What are the key skills and qualifications needed to thrive as a computational chemistry software developer?

To thrive as a Computational Chemistry Software Developer, you need a strong background in computational chemistry, programming (particularly in languages like Python, C++, or Fortran), and a relevant degree in chemistry, physics, or computer science. Familiarity with molecular modeling packages, high-performance computing environments, and version control systems such as Git is typically required. Critical thinking, teamwork, and effective communication are crucial soft skills for collaborating with interdisciplinary teams and translating scientific requirements into robust software solutions. These skills and qualifications are vital for developing reliable, efficient software tools that advance chemical research and innovation.

What are some common challenges faced by computational chemistry software developers when integrating new algorithms into existing software platforms?

Computational Chemistry Software Developers often encounter challenges when integrating new algorithms, such as ensuring compatibility with legacy code, maintaining software performance, and validating scientific accuracy. Balancing the need for cutting-edge features with stability and user-friendliness can be complex, especially in collaborative, multidisciplinary teams. Regular communication with chemists and end-users is crucial to understand requirements and to troubleshoot issues that may arise during implementation.
What are popular job titles related to Computational Chemistry Software Developer jobs in Colorado? For Computational Chemistry Software Developer jobs in Colorado, the most frequently searched job titles are:
What job categories do people searching Computational Chemistry Software Developer jobs in Colorado look for? The top searched job categories for Computational Chemistry Software Developer jobs in Colorado are:
What cities in Colorado are hiring for Computational Chemistry Software Developer jobs? Cities in Colorado with the most Computational Chemistry Software Developer job openings:
Computational Chemistry Software Developer jobs near you
Infographic showing various Computational Chemistry Software Developer job openings in Colorado as of August 2026, with employment types broken down into 80% Full Time, 9% Part Time, 2% Temporary, and 9% Contract. Highlights an 91% In-person, 3% Hybrid, and 6% Remote job distribution.

Principal Scientist, Computational Chemistry

Cogent Biosciences

Boulder, CO • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 25 days ago

Job description

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, datadriven decision making, and innovative drug design. In this role, you will directly influence discovery programs by generating actionable structurebased 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 structurebased and ligandbased 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 structurebased drug design cycles to generate hypotheses, evaluate targets, triage hits, and guide SAR exploration.
  • Present modeling insights clearly and effectively to crossfunctional 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 largescale 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 structurebased 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 opensource computational chemistry platforms preferred.
  • Strong handson 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, fragmentbased encodings).
  • A solid publication record and excellent scientific communication skills.
  • Proven effectiveness working within crossfunctional, datadriven 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. 

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. 

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