ZipRecruiter

Log In

1

Protein Design Jobs in Colorado (NOW HIRING)

Ardent Mills

Sr. Principal Scientist

Denver, CO · On-site

Design and execute experiments, develop SOPs and protocols, synthesize data, and communicate ... Demonstrated understanding of flour quality attributes, protein functionality, starch chemistry ...

Ardent Mills

Sr. Principal Scientist

Denver, CO · On-site

Design and execute experiments, develop SOPs and protocols, synthesize data, and communicate ... Demonstrated understanding of flour quality attributes, protein functionality, starch chemistry ...

Tribonet

Sr. Principal Scientist

Denver, CO · On-site

$145 - $170/hr

Design and execute experiments, develop SOPs and protocols, synthesize data, and communicate ... Demonstrated understanding of flour quality attributes, protein functionality, starch chemistry ...

Ardent Mills

Sr. Principal Scientist

Denver, CO · On-site

Design and execute experiments, develop SOPs and protocols, synthesize data, and communicate ... Demonstrated understanding of flour quality attributes, protein functionality, starch chemistry ...

Alta Resource Technologies, Inc.

Data Analyst

Boulder, CO · On-site

$100K - $150K/yr

Experimental Design and Planning: Collaborate with technical teams to ensure statistical rigor by ... Experience with common biological assays, including fluorometric assays, protein quantification, or ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

... design. The Post-Doctoral Fellow will lead independent projects exploring transient and dynamic protein states using techniques such as cryo-electron microscopy, tomography, kinetic assays, and ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

... design. The Post-Doctoral Fellow will lead independent projects exploring transient and dynamic protein states using techniques such as cryo-electron microscopy, tomography, kinetic assays, and ...

Stanford Climate Ventures

Data Analyst

Boulder, CO · On-site

$100 - $150/hr

Experimental Design and Planning: Collaborate with technical teams to ensure statistical rigor by ... Experience with common biological assays, including fluorometric assays, protein quantification, or ...

Ardent Mills

Sr. Principal Scientist

Denver, CO · On-site

$145 - $170/hr

Design and execute experiments, develop SOPs and protocols, synthesize data, and communicate ... protein functionality, starch chemistry, enzyme systems, hydrocolloids, and their impact on ...

previous page

Showing results 41-60

All JobsProtein Design JobsProtein Design Jobs in Colorado

Protein Design information

What is protein design?

Protein design is the process of creating new proteins or modifying existing ones to have specific functions or properties. This can involve using computational tools, laboratory techniques, or a combination of both to predict and engineer amino acid sequences that will fold into desired three-dimensional structures. Protein design is used in various fields, including medicine, biotechnology, and research, to develop novel enzymes, therapeutics, or materials. The field requires a strong understanding of biology, chemistry, and computer science to achieve successful outcomes.

What are the key skills and qualifications needed to thrive as a protein design scientist, and why are they important?

To thrive as a Protein Design Scientist, you need a strong background in molecular biology, biochemistry, and computational modeling, typically supported by an advanced degree in a relevant field. Proficiency with tools such as Rosetta, PyMOL, and molecular dynamics simulation software, as well as experience with protein expression and purification techniques, is essential. Analytical thinking, problem-solving, and effective communication are important soft skills to drive innovation and collaborate with interdisciplinary teams. These skills are crucial for designing functional proteins, troubleshooting experiments, and advancing research goals in biotechnology and pharmaceutical development.

What are some typical challenges faced by professionals in protein design, and how are they addressed within a team setting?

Professionals in protein design often encounter challenges such as predicting accurate protein folding, ensuring stability, and achieving desired biological activity. These complexities are typically addressed through close collaboration with computational biologists, structural biologists, and experimental scientists. Teams frequently hold cross-functional meetings to troubleshoot issues, share findings, and iterate on design strategies based on laboratory results. This collaborative environment helps leverage diverse expertise and accelerates the development of novel proteins with desired functions.

What is the difference between Protein Design vs Protein Engineering?

AspectProtein DesignProtein Engineering
Required CredentialsBiochemistry, Molecular Biology, BioinformaticsBiochemistry, Molecular Biology, Bioinformatics
Work EnvironmentResearch labs, biotech companies, academiaResearch labs, biotech companies, academia
Industry UsageDesigning novel proteins, drug development, synthetic biologyModifying existing proteins for improved function or stability

Protein Design focuses on creating new proteins with specific functions, often using computational methods. Protein Engineering involves modifying existing proteins to enhance or alter their properties. Both roles require similar skills and are used in research, biotech, and pharmaceutical industries, but their goals differ: one designs from scratch, the other optimizes existing proteins.

What are popular job titles related to Protein Design jobs in Colorado?

For Protein Design jobs in Colorado, the most frequently searched job titles are:

What job categories do people searching Protein Design jobs in Colorado look for?

The top searched job categories for Protein Design jobs in Colorado are:

What cities in Colorado are hiring for Protein Design jobs?

Cities in Colorado with the most Protein Design job openings:

Protein Design jobs near you
Infographic showing various Protein Design job openings in Colorado as of August 2026, with employment types broken down into 88% Full Time, 8% Part Time, 1% Temporary, and 3% Contract. Highlights an 82% Physical, 5% Hybrid, and 13% Remote job distribution.

Principal Scientist, Computational Chemistry

Cogent Biosciences

Boulder, CO • On-site

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 20 days ago

Key responsibilities

  • Apply structure-based and ligand-based drug design methods to support projects from hit discovery through lead optimization.

  • Collaborate with project team members to generate hypotheses, evaluate targets, triage hits, and guide SAR exploration through iterative structure-based drug design cycles.

  • Develop, refine, and maintain computational workflows on HPC Linux environments to enable scalable large-scale simulations.

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. 

Apply