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Protein Design Jobs in Colorado (NOW HIRING)

Eli Lilly and Company

Director, Medicinal Chemistry

Louisville, CO · On-site

$163K - $257K/yr

  • Medical

  • Dental

  • Vision

  • Life

  • Retirement

  • PTO

Extensive experience in medicinal chemistry, SAR analysis, and structure- and mechanism-based molecular design. * Direct experience designing oroptimizingmolecular gluedegraders, including protein ...

Eli Lilly and Company

Director, Medicinal Chemistry

Louisville, CO · On-site

$163K - $257K/yr

  • Medical

  • Dental

  • Vision

  • Life

  • Retirement

  • PTO

Extensive experience in medicinal chemistry, SAR analysis, and structure- and mechanism-based molecular design. * Direct experience designing or optimizing molecular glue degraders, including protein ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

Provide laboratory science expertise and leadership in study design, study oversight, data ... Protein engineering and biochemical assay development * Nanobody discovery, selection ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

Provide laboratory science expertise and leadership in study design, study oversight, data ... Protein engineering and biochemical assay development * Nanobody discovery, selection ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

In addition to protein-protein interactions, the lab explores the role of membrane dynamics and ... Design and execute independent projects focusing on membrane-localized signaling complexes or ...

KBI Biopharma, Inc.

Scientist I

Louisville, CO · On-site

$84K - $115K/yr

This role is ideal for a scientist with deep expertise in protein analytics, ideally with a ... Design and strategically execute analytical experiments in support of biotherapeutics development ...

University of Colorado

Post-Doctoral Fellow

Aurora, CO · On-site

$49K - $67K/yr

In addition to protein-protein interactions, the lab explores the role of membrane dynamics and ... Design and execute independent projects focusing on membrane-localized signaling complexes or ...

Cogent Scientific

Pharma Cell Biologist

Louisville, CO · On-site

  • Medical

  • Dental

  • Vision

  • Retirement

  • PTO

... protein interaction studies, RT-q-PCR, pulldown, western blotting) to support target validation and mechanistic studies. * Contributing to experimental design/execution, data interpretation ...

Cogent Scientific

Pharma Cell Biologist

Louisville, CO · On-site

$95K - $105K/yr

  • Medical

  • Dental

  • Vision

  • Retirement

  • PTO

... protein interaction studies, RT-q-PCR, pulldown, western blotting) to support target validation and mechanistic studies. * Contributing to experimental design/execution, data interpretation ...

Cogent Scientific

Pharma Cell Biologist

Louisville, CO

  • Medical

  • Dental

  • Vision

  • Retirement

  • PTO

... protein interaction studies, RT-q-PCR, pulldown, western blotting) to support target validation and mechanistic studies. * Contributing to experimental design/execution, data interpretation ...

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Showing results 1-20

All JobsProtein Design JobsProtein Design Jobs in Colorado

Protein Design information

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 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 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 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 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 83% Full Time, 7% Part Time, and 10% Contract. Highlights an 96% In-person, 2% Hybrid, and 2% Remote job distribution.

Scientist I, Computation Protein Design

Alta Resource Technologies, Inc.

Boulder, CO • On-site

$140K - $175K/yr

Full-time

Medical, Dental, Vision, Retirement

Re-posted 6 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.

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