ZipRecruiter

Log In

1

Protein Engineering Jobs in Colorado (NOW HIRING)

Cascade Bio

Process Development Scientist

Denver, CO

$110K - $150K/yr

Interface with protein engineering efforts, translating process bottlenecks into enzyme engineering targets and back-integrating improved variants * Contribute broadly across the organization: at ...

Cascade Bio

Process Development Scientist

Denver, CO · On-site

$110K - $150K/yr

Interface with protein engineering efforts, translating process bottlenecks into enzyme engineering targets and back-integrating improved variants * Contribute broadly across the organization: at ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

Protein engineering and biochemical assay development * Nanobody discovery, selection, characterization * Structural biology approaches (preferably cryo-EM) * Biophysical characterization of protein ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

Protein engineering and biochemical assay development * Nanobody discovery, selection, characterization * Structural biology approaches (preferably cryo-EM) * Biophysical characterization of protein ...

Cogent Scientific

Expert Pharma Biochemist

Louisville, CO · On-site

$40K - $54K/yr

Characterizing protein-protein interactions between targets and engineered binders using biophysical methods (mass photometry, analytical SEC, SEC-MALS, SPR, or BLI). * Preparing and optimizing ...

Cogent Scientific

Expert Pharma Biochemist

Louisville, CO · On-site

$40K - $54K/yr

Characterizing protein-protein interactions between targets and engineered binders using biophysical methods (mass photometry, analytical SEC, SEC-MALS, SPR, or BLI). * Preparing and optimizing ...

Cogent Scientific

Expert Pharma Biochemist

Louisville, CO · On-site

$115K - $125K/yr

Characterizing protein-protein interactions between targets and engineered binders using biophysical methods (mass photometry, analytical SEC, SEC-MALS, SPR, or BLI). * Preparing and optimizing ...

next page

Showing results 1-20

All JobsProtein Engineering JobsProtein Engineering Jobs in Colorado

Protein Engineering information

See Colorado salary details

$34.2K

$66.2K

$100.4K

How much do protein engineering jobs pay per year?

As of Aug 16, 2026, the average yearly pay for protein engineering in Colorado is $66,222.00, according to ZipRecruiter salary data. Most workers in this role earn between $49,400.00 and $75,700.00 per year, depending on experience, location, and employer.

What is protein engineering?

A Protein Engineering job involves designing, modifying, and optimizing proteins for specific applications in medicine, biotechnology, and industry. Scientists in this field use computational modeling, directed evolution, and genetic engineering to enhance protein functions. Roles may include developing enzymes for drug production, improving therapeutic proteins, or creating biomaterials. This work often requires expertise in molecular biology, biochemistry, and structural biology.

What are the key skills and qualifications needed to thrive in protein engineering, and why are they important?

To thrive in Protein Engineering, you need a solid background in biochemistry, molecular biology, and genetic engineering, typically supported by a relevant advanced degree. Experience with laboratory techniques such as PCR, site-directed mutagenesis, protein expression/purification, and analytical tools like mass spectrometry or chromatography is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills help you stand out in this role. These competencies are crucial for designing novel proteins, collaborating in multidisciplinary teams, and ensuring successful project outcomes in biotech or pharmaceutical environments.

What are the typical daily responsibilities of someone working in protein engineering?

A typical day in Protein Engineering involves designing and conducting experiments to modify protein sequences, expressing and purifying proteins, and analyzing their structure or function using techniques like chromatography and spectroscopy. You will often document your results, troubleshoot unexpected findings, and present data to colleagues or project teams. Collaboration with scientists in molecular biology, bioinformatics, and structural biology is common to ensure robust experimental design and data interpretation. The role may also include literature reviews to stay updated with the latest research and participating in team meetings to plan next steps or project timelines.

How much do protein engineers make?

Protein engineers typically earn a median salary ranging from $70,000 to $120,000 annually, depending on experience, education, and location. Advanced skills in molecular biology, bioinformatics, and laboratory techniques can lead to higher compensation, especially in biotech or pharmaceutical industries.

What do protein engineers do?

Protein engineers design and modify proteins to improve their functions or create new ones, often using techniques like directed evolution and computational modeling. They work in research labs, utilizing tools such as gene editing and structural analysis to develop applications in medicine, agriculture, and industry.

What are the most commonly searched types of Protein Engineering jobs in Colorado?

The most popular types of Protein Engineering jobs in Colorado are:

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

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

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

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

What cities in Colorado are hiring for Protein Engineering jobs?

Cities in Colorado with the most Protein Engineering job openings:

Protein Engineering jobs near you
Infographic showing various Protein Engineering job openings in Colorado as of August 2026, with employment types broken down into 100% Full Time. Highlights an 92% In-person, and 8% Remote job distribution, with an average salary of $66,222 per year, or $31.8 per hour.

Scientist I, Computation Protein Design

Alta Resource Technologies, Inc.

Boulder, CO • On-site

$140K - $175K/yr

Full-time

Medical, Dental, Vision, Retirement

Re-posted 9 days ago

Job description

About Alta
Alta Resource Technologies (Alta) is a next generation mining company that uses synthetic biology to separate critical minerals from conventional and unconventional resources, including e-waste. Founded in 2023, the company is expanding its team in Boulder, CO. The exponential growth of new tech industries, as well as the information technology sector, are driving historic growth in mineral demand and stressing existing supply streams. Meeting new demand, diversifying the supply chain, and producing minerals in a more sustainable manner requires the rapid development, deployment and scaling of new technologies. This mineral challenge represents a historic opportunity for technology development and value creation. Alta is proud to be at the vanguard of this mega trend.
About the Role:
We are seeking a highly skilled Scientist I, Computation Protein Design to join our team and drive innovation in protein design and engineering through good data practices, robust analytical methods and machine learning. This role focuses on leveraging and optimizing foundational AI models to accelerate our protein engineering pipeline. The ideal candidate will have deep expertise in model fine-tuning, evaluation, and selection, with strong data engineering capabilities to support cutting-edge computational biology research.
Key Responsibilities:
Model Development
  • Fine-tune, adapt, and use foundational protein models (e.g., BoltzGen, ESM, OpenFold derivatives) for protein engineering applications
  • Develop and implement rigorous evaluation frameworks to assess model performance, including metrics for protein structure prediction, sequence optimization, and functional property prediction
  • Conduct comprehensive benchmarking studies to identify and recommend the most suitable foundational models for various protein engineering tasks
  • Design and execute computational experiments to validate model predictions against experimental data
  • Leverage multiple information sources (including bioinformatic, structural, simulations, and experimental performance data) to improve internal models and develop agentic frameworks

Cross-functional collaboration
  • Collaborate with the Applied Biology team to translate models into actionable insights.
  • Create technical documentation including model assumptions, equations, validation results, and recommendations.
  • Provide technical mentorship and review for junior engineers and scientists.
  • Clearly communicate technical findings, risks and recommendations to leadership and project stakeholders.

Data Management, Analysis and Integration
  • Contribute to developing data management systems that meet FAIR principles.
  • Develop analysis code to support the team in analyzing experimental data.
  • Engineer data into vectorized format for MCP integration
  • Utilize experimental data to validate and improve model development.

Required Qualifications:
  • Ph.D. in Computational Biology, Bioinformatics, Computer Science with 1-3 years of relevant industry or post-doctoral experience, or M.S. with 6+ years of relevant industry experience
  • Hands-on experience with protein foundation models such as ESM-2, ESM-3, ProteinMPNN, RFdiffusion, AlphaFold, or similar architectures
  • Knowledge of protein design software and molecular modeling tools (Rosetta, PyMOL, Chimera)
  • Demonstrated experience fine-tuning and working with large-scale machine learning models, preferably protein or biological sequence models
  • Strong proficiency in Python and modern ML frameworks (PyTorch, TensorFlow, JAX)
  • Experience with model evaluation methodologies, including cross-validation, performance metrics, and statistical analysis
  • Solid understanding of protein structure, function, and the principles of protein engineering
  • Experience with high-performance computing environments and GPU-accelerated computing
  • Strong communication skills and ability to work collaboratively in interdisciplinary teams
  • US Citizenship required.

Preferred, But Not Required:
  • Experience with workflow management tools (Nextflow, Snakemake, or similar)
  • Familiarity with cloud computing platforms (AWS, GCP, Azure) and containerization (Docker, Singularity)
  • Experience with distributed computing frameworks (Dask, Ray, Spark)
  • Track record of publications or contributions to open-source projects in computational biology or machine learning

What We Offer:
  • The opportunity to lead a breakthrough program redefining U.S. supply chain resilience in critical materials.
  • A mission-driven, high-trust team operating at the intersection of innovation, national security, and sustainability.
  • High Impact & Visibility: Direct interaction and reporting to executive leadership.
  • Competitive compensation and benefits package.
    • The starting pay range for this position is $140,000 to $175,000 commensurate with educational background and work experience.
    • Benefits including, 401(K) medical, dental, and vision plans, or equivalent, will be provided.
    • Paid parental leave, paid sick leave, flexible time off, company holidays.

EOE
Alta Resource Technologies is an equal opportunity employer committed to building a workforce that reflects the diversity of the communities we serve. We believe that varied perspectives, experiences, and backgrounds strengthen our team and drive better outcomes for our clients and partners.
We welcome and encourage applications from all qualified individuals regardless of race, color, religion, gender, sexual orientation, gender identity, national origin, age, disability, veteran status, or any other characteristic protected by law. Our hiring decisions are based solely on qualifications, merit, and the needs of the business. Alta participates in e-Verify for all positions.
If you require accommodations at any point in the hiring process, please let your recruiter know.
For information about Alta's privacy practices, see our Privacy Policy.

Apply