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Protein Design Jobs (NOW HIRING)

Arcadia Science

Protein Designer

Emeryville, CA · On-site

$130K - $180K/yr

Our Validation team does this by closing the design-build-test-learn loop through lab validation across diverse organisms. Read more about our work through our publications. We are seeking a Protein ...

Arcadia Science

Protein Designer

Emeryville, CA

$130K - $180K/yr

Our Validation team does this by closing the design-build-test-learn loop through lab validation across diverse organisms. Read more about our work through our publications. We are seeking a Protein ...

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Protein Design information

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$42K

$114.5K

$201.5K

How much do protein design jobs pay per year?

As of Jun 21, 2026, the average yearly pay for protein design in the United States is $114,491.00, according to ZipRecruiter salary data. Most workers in this role earn between $83,500.00 and $144,000.00 per year, depending on experience, location, and employer.

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.
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Protein Design jobs near you

Senior AI Peptide and Protein Design Engineer

Ellison Institute, LLC

Los Angeles, CA • On-site

$160K - $213K/yr

Full-time

Posted 8 days ago

Job description

Job Title: Senior AI Peptide and Protein Design Engineer
Annual Base Salary: DOE, $160,000-$213,000 along with bonus eligibility and a comprehensive benefits package
Location: Los Angeles, CA
Our Mission
Formerly known as the Ellison Institute of Technology Los Angeles, the Ellison Medical Institute strives to spark innovation, leverage technology, and drive interdisciplinary, patient-centered research to continually enhance health, reimagine and redefine cancer care, and transform lives.
Established in 2016 as a medical research and development center, the Institute features innovation labs for artificial intelligence and molecular analytics and was among the first organizations to vertically integrate the interdisciplinary study and treatment of disease. We offer multifaceted programs, including a preventative medicine and cancer clinic, cross-disciplinary research laboratories, a health policy think-tank, and community outreach and educational programs.
Please visit emila.org for more details.
Job Summary
The Ellison Medical Institute is launching a strategic new initiative in de novo peptide and protein engineering to advance the design and delivery of next-generation therapeutics. This effort represents a deliberate expansion of the organization's capabilities and will establish a strong foundation in AI-driven peptide and protein engineering.
The successful candidate will play a central role in shaping core tools, workflows, and technical direction, while working closely with experts in peptide and protein design who are deeply engaged in the program. The Senior AI Peptide and Protein Design Engineer role offers the opportunity to influence the initiative from its inception with strong scientific partnership and institutional support. Candidates with strong peptide and protein design backgrounds are encouraged to apply.
Why You Should Join Us:
  • Build a Foundational Capability: Help establish and scale core AI-driven peptide and protein engineering capabilities from the ground up.
  • Translational Focus: Work on technologies designed to directly influence therapeutic discovery and development across multiple programs.
  • Cross-Functional Collaboration: Work in a highly integrated environment with physicians, computational scientists, peptide and protein characterization and experimental teams to translate designs from concept to therapeutic candidates.
  • High Ownership and Impact: Shape tools, workflows, and technical direction with visibility across research and leadership.
Job Accountabilities:
  • De Novo Design Pipelines: Develop, deploy, and continuously improve computational pipelines for de novo peptide and protein design, including property prediction using data-driven and modeling approaches. Define robust benchmarking, performance metrics, and validation strategies.
  • Peptide and Protein Design: Design and optimize novel peptide and protein therapeutics using sequence- and structure-based computational design methods, leveraging silico predictions to support lead identification and optimization.
  • Design-Build-Test Cycles: Work directly with the peptide and protein production and characterization teams to experimentally test designs, interpret results, and incorporate feedback into iterative design cycles.
  • Cross-Functional Integration: Collaborate with target biology and translational research teams to evaluate designs in biological context and support progression from concept to optimized lead candidates.
  • Mentorship: Mentoring junior scientists or contributing to hiring and team growth.
  • Documentation & Communication: Maintain clear, reproducible documentation of methodologies, code, and results. Communicate findings effectively to scientific and leadership stakeholders.
  • Culture & Leadership: Contribute to a high-performing scientific culture that values rigor, innovation, transparency, collaboration, accountability, and efficient execution.
ADDITIONAL INFORMATION
  • Required Education: Ph.D. in Computational Peptide/Protein Design, Structural Biology, Protein Engineering, or a closely related field.
  • Required Experience:
    • Postdoctoral or industry experience applying computational modeling to peptide or protein engineering, and a strong publication record or proven track record contributing to therapeutic development.
    • 5+ years of hands-on experience in peptide and protein design, modeling, and sequence/structure-function prediction, with proficiency in relevant. macromolecular modeling software (i.e. AlphaFold, RoseTTAFold, RFdiffusion, RFpeptides, Boltz, ProteinMPNN).
    • Demonstrated understanding of peptide and protein biology, including structure, folding, stability, and experimental constraints, gained through direct experimental work and/or close collaboration with wet-lab teams.
    • Strong analytical and problem-solving skills applied to complex biological and computational challenges.
    • Excellent teamwork, time management, documentation, and communication skills
    • Proven ability to work effectively in interdisciplinary, cross-functional research environments.
For the safety and health of employees, guests, and patients, the Ellison Medical Institute may mandate vaccination requirements for employment. The Ellison Medical Institute's policies are always subject to review and change to ensure they are appropriate under the circumstances.
The Ellison Medical Institute is an equal opportunity employer. We believe that an inclusive, collaborative team environment is just as important to our mission as stethoscopes and microscopes. We strive to always provide employees a supportive atmosphere, so they feel confident taking creative risks toward innovation. The Ellison Medical Institute values emotional intelligence and communication with empathy and respect for others. We seek to build a diverse group of people who are curious, have a deep sense of responsibility, and the grit needed to achieve excellence.

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