Senior / Principal Scientist, AI for Protein Engineering

Lila Sciences

Salary: $268k - $358k
Location: Cambridge or San Francisco
Job type: Full-time

Required skills

biotechnology
computational biology
end-to-end
machine learning
predictive models

About the role

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.

About Lila Sciences

Develops an AI platform for autonomous scientific research and discovery.

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