Scientist II, ML - Guided Protein Design Evaluation

profluent

Emeryville, California, United States; Hybrid (2-3 days on-site) · Emeryville · United States; Hybrid (2-3 days on-site)

Posted Jun 24, 2026

Other
Machine Learning

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Job description

Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in 2022 and headquartered in Emeryville, CA, Profluent is backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures and has raised over $150M to date.

We are expanding the ML Design Evaluation (MDE) program; the cross-functional program that runs dedicated, structured design campaigns to generate high-quality experimental data for Profluent’s protein design models. MDE sits at the intersection of ML, Biology, and Bioinformatics, and its output directly translates into improved models and accelerated protein design campaigns.

We are looking for a scientist with deep expertise in therapeutic antibody development, protein engineering, and ML-guided protein design to partner with the MDE Lead on the scientific substance of the program. You will own the translation between what our ML team needs to learn from each campaign and what the experimental system (internal assays and CRO-run workflows) can deliver. You will help scope targets and assays, partner with ML scientists to define what “model-ready” data looks like for each campaign, set and enforce assay readiness and QC expectations, and close the Design→ Build→ Test→ Learn loop by tracking how each dataset impacts model performance.

This is a hands-on technical role, not a pure program role. You’ll collaborate with ML and Protein Design scientists to develop experimental designs, review assay protocols, troubleshoot data quality issues with internal teams and CROs, and work closely with ML scientists to understand how data is used in model training.

Responsibilities

Partner with ML and Protein Design leads to scope MDE campaigns; including target selection, choice of assays, and what readouts are needed to improve the next generation of models
Define assay readiness levels, controls, and QC acceptance criteria for each campaign, and enforce them across internal execution and external CROs
Review incoming data (biochemical, biophysical, NGS-based screens) for scientific soundness before it is accepted into the data warehouse and used for model training
Work with Bioinformatics on metadata schemas and data ingestion so that every dataset is consistent, queryable, and traceable back to its parent project.
Serve as the scientific point of contact for CRO technical scoping; evaluate whether a vendor’s platform, assay conditions, and controls are fit for purpose for ML-guided optimization
Contribute to campaign charters, benchmarking assay design, and post-campaign readouts; help turn individual experiments into a growing institutional dataset
Represent the MDE program in cross-functional technical forums and help raise the data-quality bar across the organization

Qualifications

PhD in Molecular Biology, Biochemistry, Protein Engineering, Biophysics, Immunology, or a closely related field; or MS with equivalent industry experience
5+ years of hands-on experience with protein engineering and functional characterization, including biochemical activity, binding, stability, and/or expression assays
Direct experience with therapeutic antibody discovery and engineering (e.g., affinity maturation, developability optimization, humanization, format engineering) and the assays that support it (binding kinetics, epitope characterization, biophysical and developability panels)
Strong working knowledge of NGS-based screening workflows (e.g., deep mutational scanning, amplicon sequencing, high-throughput activity screens, antibody display library sequencing) and what makes that data usable for modeling
Demonstrated ability to define assay quality standards (signal/noise, reproducibility, plate-level controls) and hold experimental workflows to them
Fluent working across scientific disciplines; can talk protein chemistry and antibody biology with biologists and model-guided design approaches with ML scientists without losing either audience

Preferences

Prior experience closing Design–Build–Test–Learn loops in an industrial protein design, antibody engineering, or directed evolution setting
Experience with display-based antibody discovery platforms (phage, yeast, mammalian) and/or single-cell B-cell screening workflows
Experience scoping and overseeing externally run assays at CROs, including technical evaluation of vendor platforms
Comfortable with Python/pandas and SQL at the level needed to inspect, QC, and reason about experimental datasets independently
Familiarity with LIMS and project-management systems and experience defining data & metadata schemas for experimental data
Exposure to kinases, nucleases, recombinases, or gene editing enzymes is a plus
Track record of publishing, presenting, or shipping work at the intersection of protein engineering and machine learning

What We Offer

High-growth opportunity with meaningful impact on the future of protein design
Competitive compensation package with equity participation
401(k) with a strong employer match
Comprehensive benefits including health/dental/vision insurance
Generous PTO policy and commitment to work-life balance
Professional development opportunities in a cutting-edge field at the intersection of AI and biology

Profluent Bio, Inc is an equal opportunity employer promoting diversity and inclusion in the workspace. We do not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical conditions, veteran status, sexual orientation, gender (including gender identity and gender expression), sex (which includes pregnancy, childbirth, and breastfeeding), genetic information, taking or requesting statutorily protected leave, or any other basis protected by law.

Work Authorization Requirement

Applicants must have ongoing work authorization in the United States that does not require employer sponsorship. Sponsorship will not be provided now or at any time in the future for this position.

Employment Eligibility Verification

Legal authorization to work in the United States is required. In compliance with federal law, all persons hired must verify their identity and work eligibility and complete the required employment verification form upon hire.

Hiring Salary Range

$147,000—$180,000 USD