Assistant Director Protein Engineering Jobs (NOW HIRING)

The heart of Prellis Bio’s strategy is the combination of novel, cutting‑edge methods in machine learning, biology at scale, and next‑gen antibody discovery that address long-standing industry‑wide problems in the drug development pipeline. Prellis Biologics uses proprietary technology to 3D print human lymph node organoids, enabling the rapid & diverse discovery of human antibody therapeutic candidates for a range of applications. To drive this forward, we are assembling an incredible team of discovery biologists, computational scientists, and protein scientists who want to make a difference to this important problem.

We are seeking a Senior / Principal Scientist — Antibody Protein Engineering to join our High Throughput Discovery group. You will drive antibody design and optimization, maturing early hits into development‑ready leads. You will be responsible for:

• Leading late-stage antibody design and optimization — affinity maturation, Fc engineering, and developability polishing to advance lead candidates toward development.
• Building an integrated wet‑lab + computational engineering platform — biologics reformatting, multispecific assembly, screening & library design (high‑diversity libraries, focused‑library maturation, ML training‑data campaigns), and computational design.

The ideal candidate will thrive in a dynamic, hands‑on environment and play a critical role in delivering life‑changing therapeutics.

• Lead antibody engineering with a strong emphasis on late-stage design and optimization to refine and advance lead candidates toward development. Core activities: Reformat biologics across modalities (scFv, scFv‑Fc, minibodies, Fab, VHH, Fc fusions, albumin fusions, TCRm) and assemble multispecifics (knob‑in‑hole, CrossMab, DVD‑Ig, common LC, DARTs)
• Fc engineering — mutations for half‑life, effector‑function modulation, isotype selection, and bispecific heterodimerization
• Affinity maturation — design focused libraries to improve affinity, kinetics, and specificity
• Polishing & developability — remove chemical liabilities, mitigate aggregation and immunogenicity, humanize when needed
• Screening & library construction — design and execute campaigns (alanine scanning, high‑diversity libraries via PCR, Gibson, mutagenesis, oligo‑pool synthesis); generate ML training‑data campaigns; translate manual workflows to automation
• Computational design — apply structural tools (PyMOL, Schrödinger BioLuminate / Maestro) and partner with Data Science / AI/ML on protein language and structure models (AlphaFold, ESM, RFdiffusion, ProteinMPNN, or equivalent)

• Ph.D. in Biochemistry, Bioengineering, Molecular Biology, Protein Engineering, or related field with equivalent industry experience: Sr. Scientist (PhD + 3‑5 yrs); Principal Scientist (PhD + 5+ yrs)
• Hands‑on biologics reformatting across scFv, scFv‑Fc, Fab, Fc fusions, VHH, and Fc engineering
• Demonstrated experience optimizing / engineering antibody lead candidates (affinity, developability, and Fc properties) and hands‑on experience with biologics screening using iQue and MACSQuantor high content imaging (HCI).
• Computational fluency: PyMOL, Schrödinger (BioLuminate / Maestro), molecular dynamics, or equivalent, and at least one protein language model (ESM, RFdiffusion, ProteinMPNN, or equivalent)
• Strong molecular cloning, mutagenesis, and DNA library construction
• Mentorship of junior researchers; clear scientific communication; track record of publications, presentations, or patents
• Experience managing external vendors (CROs / CDMOs) for biologics production and characterization
• Thrive in cross‑functional collaboration

• Strong background in antibody discovery pipelines: expression, purification, screening, and analytical characterization.
• Experience continuous directed evolution (OrthoRep, PACE): high‑diversity libraries (yeast, ribosome, mRNA, mammalian), multi‑round selection, and quantitative affinity binning liquid‑handling automation (Biomek, Lynx, Tecan), LIMS / ELN (Benchling)

At Prellis we integrate human biology with machine learning. We aim to revolutionize drug discovery by harnessing the power of the human immune system with tightly integrated machine learning to develop next‑generation antibody therapeutics with unparalleled speed, precision, and safety. We are committed to empowering our pharmaceutical partners with access to the most promising fully human antibody candidates rapidly identified from the human immune repertoire, enabling them to bring life‑changing treatments to patients faster than ever before. Prellis Biologics is a pre‑IPO biotech located in Berkeley, CA with a team‑oriented, inclusive, and family‑friendly culture. Our growing pipeline targets high unmet patient needs across therapeutic areas including metabolic disease, inflammation, and oncology. Prellis has raised funding from top investors, including Celesta, Khosla Ventures, SOSV, and Avidity Partners.

As we work to develop treatments that take care of others, we also work to care for your professional and personal growth and well‑being. From our competitive benefits to our collaborative culture, we’ll support your journey every step of the way.

Actual salary will vary based on several factors including, but not limited to, relevant skills, experience, and qualifications.

In addition to the base salary, Prellis offers compelling benefits based on eligibility, comprising health and welfare plans for staff and eligible dependents, financial plans with opportunities to save toward retirement or other goals, work/life balance, and career development opportunities that may include:

• A competitive employee benefits package, including group medical, dental, and vision coverage, life and disability insurance, flexible spending accounts, and a 401(k) plan
• Stock‑based long‑term incentives
• Holiday package including a 1+ week winter shutdown
• Flexible work models, including remote and hybrid working arrangements, where possible

Prellis does not have an application deadline for this position; we will continue accepting applications until we receive a sufficient number or select a candidate for the position.

Prellis Bio is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran, or disability status.

We believe diversity, equity, and inclusion need to be at the foundation of our culture. We work hard to bring together diverse teams — grounded in a wide range of expertise and life experiences — and work even harder to ensure those teams thrive in inclusive, growth‑oriented environments supported by equitable company and team practices. All candidates can expect equitable treatment, respect, and fairness throughout the interview process.