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Protein Engineering Jobs in Boston, MA (NOW HIRING)

Jj

Director, Protein Sciences

Cambridge, MA

The Director, Protein Sciences will integrate target biology insight, computational protein design, cell engineering, and experimental protein sciences to drive the generation of high-quality ...

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Protein Engineering information

See Boston, MA salary details

$35.3K

$68.4K

$103.7K

How much do protein engineering jobs pay per year?

As of Jul 29, 2026, the average yearly pay for protein engineering in Boston, MA is $68,407.00, according to ZipRecruiter salary data. Most workers in this role earn between $51,100.00 and $78,200.00 per year, depending on experience, location, and employer.

What is a Protein Engineering job?

A Protein Engineering job involves designing, modifying, and optimizing proteins for specific applications in medicine, biotechnology, and industry. Scientists in this field use computational modeling, directed evolution, and genetic engineering to enhance protein functions. Roles may include developing enzymes for drug production, improving therapeutic proteins, or creating biomaterials. This work often requires expertise in molecular biology, biochemistry, and structural biology.

What are the key skills and qualifications needed to thrive in the Protein Engineering position, and why are they important?

To thrive in Protein Engineering, you need a solid background in biochemistry, molecular biology, and genetic engineering, typically supported by a relevant advanced degree. Experience with laboratory techniques such as PCR, site-directed mutagenesis, protein expression/purification, and analytical tools like mass spectrometry or chromatography is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills help you stand out in this role. These competencies are crucial for designing novel proteins, collaborating in multidisciplinary teams, and ensuring successful project outcomes in biotech or pharmaceutical environments.

What are typical daily responsibilities for someone working in Protein Engineering?

A typical day in Protein Engineering involves designing and conducting experiments to modify protein sequences, expressing and purifying proteins, and analyzing their structure or function using techniques like chromatography and spectroscopy. You will often document your results, troubleshoot unexpected findings, and present data to colleagues or project teams. Collaboration with scientists in molecular biology, bioinformatics, and structural biology is common to ensure robust experimental design and data interpretation. The role may also include literature reviews to stay updated with the latest research and participating in team meetings to plan next steps or project timelines.

What are the most commonly searched types of Protein Engineering jobs in Boston, MA? The most popular types of Protein Engineering jobs in Boston, MA are:
What are popular job titles related to Protein Engineering jobs in Boston, MA? For Protein Engineering jobs in Boston, MA, the most frequently searched job titles are:
What job categories do people searching Protein Engineering jobs in Boston, MA look for? The top searched job categories for Protein Engineering jobs in Boston, MA are:
What cities near Boston, MA are hiring for Protein Engineering jobs? Cities near Boston, MA with the most Protein Engineering job openings:
Protein Engineering jobs near you
Infographic showing various Protein Engineering job openings in Boston, MA as of July 2026, with employment types broken down into 98% Full Time, and 2% Contract. Highlights an 98% In-person, and 2% Hybrid job distribution, with an average salary of $68,407 per year, or $32.9 per hour.

Director, Computational & Protein Sciences

Stylus Medicine

Cambridge, MA

$245K - $265K/yr

Other

Posted 25 days ago

Job description

About the Role:

Stylus Medicine is seeking an intellectually curious and creative Director, who will serve as a key scientific leader on our Platform team, owning the computational strategy that drives large serine recombinase (LSR) engineering and clinical translation. This role sits at the intersection of protein engineering, multi-omics analysis, and AI/ML-driven design and will lead a high-impact team spanning NGS and computational biology while driving the analytical infrastructure and predictive capabilities needed to advance our proprietary LSR platform from discovery through translation.

Key Responsibilities & Accountabilities:

  • Lead and develop a team of NGS and computational biology scientists, setting technical direction, mentoring team members, and fostering a collaborative, high-performance culture
  • Lead computational efforts to design and optimize LSRs and related genome engineering proteins for genetic medicine applications, integrating sequence-function, structure-function, and protein-DNA interaction datasets to guide engineering campaigns
  • Lead analysis of NGS data from LSR experiments - including amplicon sequencing, WGS, hybrid capture, and long-read sequencing - to quantify on-target efficiency and genome-wide specificity
  • Build, apply, and critically evaluate predictive and generative models for protein variant and library design - including rigorous benchmarking of AI/ML approaches such as protein language models, structure prediction tools, and generative design frameworks
  • Integrate proprietary screening data with public evolutionary and structural datasets to prioritize variants and identify engineering levers for activity, specificity, and developability
  • Oversee the design, implementation, and deployment of robust, scalable computational pipelines for multi-omics data analysis, ensuring accuracy, reproducibility, and maintainability
  • Provide scientific input into platform strategy, translating computational insights into actionable directions for the broader team
  • Partner closely with the Screening, Genome Engineering, and NGS teams to design experiments, interpret complex datasets, and refine engineering hypotheses
  • Contribute to patent filings, regulatory submissions, and publications

Qualifications & Skills:

  • PhD in Computational Biology, Bioinformatics, Protein Engineering, Machine Learning or a related quantitative discipline, with 10+ years or Master's with 14+ years of industry experience
  • Demonstrated research in protein modeling, protein design, or computational biology through publications, preprints, or equivalent industry contributions
  • Hands-on experience applying AI/ML methods to protein variant and library design, including protein language models, structure prediction, and generative design approaches (e.g., AlphaFold2/3, RFdiffusion, ProteinMPNN, ESM)
  • Expert-level proficiency in Python and/or R, with deep familiarity with data science libraries (e.g., Pandas, NumPy, Bioconductor, SciPy, PyTorch, or JAX)
  • Experience with cloud computing platforms and workflow management systems
  • Excellent communication and documentation skills, with a track record of effective collaboration in fast-paced, interdisciplinary environments

Pay Range; $245,000 - $265,000

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