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Senior Protein Engineer Jobs (NOW HIRING)

CEDENT

Senior Scientist

Branford, CT · On-site

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... If you're a protein engineer who thrives in the lab and wants your work to move swiftly toward ...

CEDENT

Senior Scientist (Branford, CT)

Branford, CT · On-site

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... If you're a protein engineer who thrives in the lab and wants your work to move swiftly toward ...

Cedent

Senior Scientist (Branford, CT)

Branford, CT · On-site

$90K - $123K/yr

We're hiring a Senior or Principal Scientist to join our Biotherapeutics team's collaborative group ... If you're a protein engineer who thrives in the lab and wants your work to move swiftly toward ...

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Senior Protein Engineer information

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$59.5K

$126.6K

$183.5K

How much do senior protein engineer jobs pay per year?

As of Jun 6, 2026, the average yearly pay for senior protein engineer in the United States is $126,557.00, according to ZipRecruiter salary data. Most workers in this role earn between $104,500.00 and $143,500.00 per year, depending on experience, location, and employer.

What is the difference between Senior Protein Engineer vs Protein Scientist?

AspectSenior Protein EngineerProtein Scientist
Required CredentialsBachelor's or Master's in Biochemistry, Molecular Biology, or related fields; experience in protein engineeringBachelor's or Master's; often a Ph.D. for advanced research roles; expertise in protein analysis
Work EnvironmentBiotech or pharmaceutical R&D labs, manufacturing facilitiesAcademic labs, research institutions, biotech companies
Employer & Industry UsageUsed in biotech, pharma, and industrial enzyme companiesCommon in academic research, biotech R&D, and pharmaceutical development

While both roles focus on proteins, Senior Protein Engineers typically work on designing and optimizing proteins for industrial applications, whereas Protein Scientists often conduct fundamental research to understand protein functions. The roles overlap in skills and industry but differ in focus and seniority.

What are Senior Protein Engineers?

Senior Protein Engineers are experienced scientists who design, modify, and optimize proteins for specific industrial, medical, or research applications. They use advanced techniques in molecular biology, biochemistry, and computational modeling to improve protein stability, activity, or specificity. These professionals often lead research projects, mentor junior staff, and collaborate with interdisciplinary teams to bring innovative protein-based solutions to market.

What are the key skills and qualifications needed to thrive as a Senior Protein Engineer, and why are they important?

To thrive as a Senior Protein Engineer, you need expertise in protein biochemistry, molecular biology, and structural biology, typically supported by a Ph.D. or equivalent experience in a related field. Proficiency in tools such as protein modeling software (e.g., Rosetta, PyMOL), high-throughput screening platforms, and familiarity with analytical instruments like mass spectrometers is essential. Strong problem-solving, collaboration, and project management skills help drive innovation and successful cross-functional teamwork. These skills and qualities are crucial for efficiently designing, optimizing, and characterizing proteins to advance scientific discoveries and product development.

How does a Senior Protein Engineer typically collaborate with cross-functional teams during the development of new protein therapeutics?

Senior Protein Engineers often work closely with multidisciplinary teams, including molecular biologists, biochemists, computational scientists, and regulatory specialists, to bring new protein therapeutics from concept to reality. They contribute their expertise in protein design and engineering, lead experimental planning, and interpret complex data to guide project direction. Regular meetings and collaborative problem-solving sessions are common, ensuring that project goals align across departments. This collaborative environment fosters innovation, but also requires strong communication and project management skills.
More about Senior Protein Engineer jobs
What cities are hiring for Senior Protein Engineer jobs? Cities with the most Senior Protein Engineer job openings:
What are the most commonly searched types of Protein Engineer jobs? The most popular types of Protein Engineer jobs are:
What states have the most Senior Protein Engineer jobs? States with the most job openings for Senior Protein Engineer jobs include:
What job categories do people searching Senior Protein Engineer jobs look for? The top searched job categories for Senior Protein Engineer jobs are:
Senior Protein Engineer jobs near you
Infographic showing various Senior Protein Engineer job openings in the United States as of May 2026, with employment types broken down into 92% Full Time, 7% Part Time, and 1% Contract. Highlights an 90% Physical, 1% Hybrid, and 9% Remote job distribution, with an average salary of $126,557 per year, or $60.8 per hour.

Senior / Principal Scientist, AI for Protein Engineering

Lila Sciences

San Francisco, CA • On-site

$268K - $358K/yr

Full-time

Medical, Dental, Vision, Life

Posted 2 days ago

Job description

Your Impact at LILA
Lila is building a platform where AI and automation co-evolve to solve the hardest problems in medicine. Within Life Sciences AI (LSAI), the AI for Protein Engineering team develops and uses the generative and predictive models that drive Lila's biomolecule design programs from in silico hypothesis to wet-lab validated lead.
We are seeking a Senior or Principal Scientist to join this team as a senior IC focused on antibody design and engineering. You will develop and execute the methods and workflows that ensure successful completion of antibody campaigns. Scope may expand to additional modalities such as enzymes and peptides as needs evolve.
This role sits at the bilingual edge of ML and biology. You will own biological understanding of campaign needs and partner closely with the Life Science Research team to design and validate computational predictions in the lab. You will shape the technical agenda for AI protein engineering at Lila and represent that work both internally and to the broader research community.
What You'll Be Building
  • Develop and own protein design and engineering workflows for antibody campaigns, including de novo design, affinity maturation, and developability optimization
  • Execute design workflows end-to-end for active campaigns and deliver wet-lab-validated leads against program milestones
  • Translate campaign requirements - epitope selection, affinity targets, biophysical constraints, and developability criteria - into well-defined ML problems and design specifications
  • Adapt and extend state-of-the-art AI methods (generative models, protein language models, structure-conditioned design) to the specific demands of antibody and broader biomolecule engineering
  • Partner with the Life Science Research team on design validation, building active learning loops where wet-lab data refines and improves model performance
  • Expand the protein engineering platform to additional modalities such as enzymes and peptides as needs evolve

What You'll Need to Succeed
  • PhD in Computational Biology, Computer Science, Machine Learning, Biophysics, or a related quantitative field
  • Proven track record of successful design of wet-lab-validated biomolecules through AI, with industry experience strongly preferred
  • Deep ML expertise with the ability to modify and adapt state-of-the-art AI approaches for protein engineering, not just apply them off-the-shelf
  • Strong fluency across both ML and protein biology, with hands-on understanding of antibody design
  • Demonstrated ability to drive a research and engineering program independently, from problem definition through experimental validation and iteration
  • Track record of close collaboration with experimental scientists and clear communication across the ML/biology boundary

Bonus Points For
  • Direct experience designing antibodies, nanobodies, or other therapeutic proteins for clinical or therapeutic pipelines
  • Experience with structure prediction, generative protein design (diffusion, flow-matching, or similar), and protein language models in a production research setting
  • Experience in structural biology and conformational dynamics
  • Experience extending design methods to additional modalities such as enzymes, peptides, or other engineered biomolecules
  • High-impact publications or open-source contributions in AI for Science (NeurIPS, ICML, ICLR, Nature Methods, Nature Biotechnology, or equivalent)
  • Experience designing or operating active learning loops between computational design and high-throughput experimental validation

Compensation
We offer competitive base compensation with bonus potential and generous early-stage equity. Your final offer will reflect your background, expertise, and expected impact.
U.S. Benefits. Full-time U.S. employees receive a comprehensive benefits program including medical, dental, and vision coverage; employer-paid life and disability insurance; flexible time off with generous company wide holidays; paid parental leave; an educational assistance program; commuter benefits, including bike share memberships for office based employees; and a company subsidized lunch program.
International Benefits. Full-time employees outside the U.S. receive a comprehensive benefits program tailored to their region. USD salary ranges apply only to U.S.-based positions; international salaries are set to local market.
Expected Base Salary Range
$268,000-$358,000 USD
About LILA
Lila Sciences is building Scientific Superintelligence™ to solve humankind's greatest challenges. We believe science is the most inspiring frontier for AI. Rather than hard-coding expert knowledge into tools, LILA builds systems that can learn for themselves.
LILA combines advanced AI models with proprietary AI Science Factory™ instruments into an operating system for science that executes the entire scientific method autonomously, accelerating discovery at unprecedented speed, scale, and impact across medicine, materials, and energy. Learn more at www.lila.ai.
Guided by our core values of truth, trust, curiosity, grit, and velocity, we move with startup speed while tackling problems of historic importance. If this sounds like an environment you'd love to work in, even if you don't meet every qualification listed above, we encourage you to apply.
We're All In
Lila Sciences is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.
Information you provide during your application process will be handled in accordance with our Candidate Privacy Policy.
A Note to Agencies
Lila Sciences does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Lila Sciences or its employees is strictly prohibited unless contacted directly by Lila Science's internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Lila Sciences, and Lila Sciences will not owe any referral or other fees with respect thereto.

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