Senior Scientist, Computational Protein Design
Clinical-stage generative biology company founded in 2018, designing protein medicines with machine learning, Boston area
| Employer | Clinical-stage generative biology company founded in 2018, designing protein medicines with machine learning, Boston area (not named) |
|---|---|
| Location | Somerville, MA (Boston) · Hybrid |
| Type & level | Full-time · Senior |
| Pay | Not stated in the posting · BLS median for medical scientists: USD 103,410 Source: U.S. Bureau of Labor Statistics, Occupational Outlook Handbook (2025 national median); the source posting states no pay |
| Visa path | O-1A fit |
| Role family | Protein Design & Structural Biology Scientist |
About the role
This scientist develops reusable computational methods, benchmarks and agentic workflows for designing and optimizing therapeutic proteins. Modeling, design, high-throughput experiments and structural work sit in one organization, so methods get tested against in-house data. The role turns successful research into dependable capabilities that program teams can use across targets.
What you'll do
- Identify capability gaps in protein engineering, form testable hypotheses, and run projects from computational work to experimental proof of concept.
- Develop generative, predictive and biophysical methods for protein design, optimization and interaction modeling.
- Build scores, benchmarks and evaluation protocols that expose failure modes and quantify uncertainty.
- Work with assay and structural scientists on molecular libraries and iterative design-build-test-learn studies.
- Create agentic and multi-agent systems that link models, internal data and experimental results, with human oversight and traceability.
- Document methods and reference workflows so program teams can adopt them, and help engineers turn research into maintainable software.
Requirements
- PhD in a relevant scientific or engineering field with at least three years of industry experience after the degree.
- Fluency in machine learning and computational methods for protein science, molecular modeling or biological design.
- Strong Python skills and experience with PyTorch or JAX, writing reliable code in a shared environment.
- Experience designing benchmarks, including dataset construction, baselines, metric validation and failure analysis.
- Solid understanding of protein structure, sequence-structure-function relationships and biophysics.
- Experience working with ML researchers, engineers and experimental scientists on applied therapeutic problems.
Nice to have
- Experience building LLM-enabled agents or multi-agent systems for therapeutic design or hypothesis testing.
- Background in protein or antibody engineering, structure-guided optimization or generative design.
Pay & benefits
Not stated in the posting · BLS median for medical scientists: USD 103,410. The posting does not list benefits.
Pay source: U.S. Bureau of Labor Statistics, Occupational Outlook Handbook (2025 national median); the source posting states no pay. Market data, not an offer from O1DMatch.
Visa path
Scientists in computational protein design commonly document O-1A evidence such as first-author publications, citations, patents, peer review, open-source tools, and conference talks. The posting states no citizenship restriction. An employer like this or a U.S. agent can file the petition, and approval depends on the individual's record.
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