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Protein Engineering Jobs in Boston, MA (NOW HIRING)

These capabilities support programs across discovery, protein engineering, immunology, and developability by transforming experimental data into actionable predictive models and scientific software.

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Protein Engineering information

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$35.3K

$68.4K

$103.7K

How much do protein engineering jobs pay per year?

As of Aug 14, 2026, the average yearly pay for protein engineering in Boston, MA is $68,415.00, 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 protein engineering?

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 protein engineering, 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 the typical daily responsibilities of 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.

How much do protein engineers make?

Protein engineers typically earn a median salary ranging from $70,000 to $120,000 annually, depending on experience, education, and location. Advanced skills in molecular biology, bioinformatics, and laboratory techniques can lead to higher compensation, especially in biotech or pharmaceutical industries.

What do protein engineers do?

Protein engineers design and modify proteins to improve their functions or create new ones, often using techniques like directed evolution and computational modeling. They work in research labs, utilizing tools such as gene editing and structural analysis to develop applications in medicine, agriculture, and industry.

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 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:

Infographic showing various Protein Engineering job openings in Boston, MA as of August 2026, with employment types broken down into 90% Full Time, 5% Part Time, 4% Contract, and 1% Nights. Highlights an 86% Physical, 4% Hybrid, and 10% Remote job distribution, with an average salary of $68,415 per year, or $32.9 per hour.

Raven StealthCo - Scientist, Conjugation Chemistry

Raven

Boston, MA โ€ข On-site

Full-time

Re-posted 12 days ago


Job description

Company Background

We are a well-funded, stealth-mode biotechnology focused on next generation oligo-based modalities targeting tissues beyond the liver, muscle, and kidney. We are building
a platform to deliver oligos with high precision to previously untargeted cells, whileย focused on "undruggable" genes, alone or in combination with previously validatedย targets. Many of our targets carry "pipeline-in-a-drug" potential: a single gene or proteinย with meaningful biological effects across multiple disease areas. Headquartered inย Cambridge, Massachusetts, the company was incubated in RA Capital's venture groupย (Raven) and is led by an experienced CEO. After a robust incubation and vettingย process, Raven StealthCo was launched and funded by RA Capital.ย The company's therapeutic areas of interest lie outside commonly targeted cells andย tissues, and represent multi-billion-dollar markets that are continuing to grow as the
population ages. Our initial focus is creating transformational therapies to treat diseases, but given the platform potential, we have longer-term ambitions to address healthy aging. These targets are backed by strong biological and genetic evidence but have historically resisted small molecule and biologic approaches. Raven StealthCo is moving quickly to address multiple disease indications at scale and with significant market potential.

Opportunity

We are in the discovery stage and will invest heavily in its emerging platform for oligonucleotide delivery. Our disease focus offers strong translatability from animal models to humans, which provides a potentially rapid and efficient path to the clinic. Given our recent funding and commitment to building a first-in-class platform with clear therapeutic targets and indications, we are recruiting a Scientist, Conjugation Chemistry. This individual will be responsible for technical planning and production of our antibody/peptide-oligonucleotide conjugates for our targeted delivery platform.

The Position

Theย Scientist, Conjugation Chemistry will report directly to the Director of Oligonucleotide and Conjugation Chemistry and will interface frequently with members of the delivery group and cross-functional teams to advance oligonucleotide therapeutic programs. This individual will help define and execute the chemical strategy to produce oligonucleotide conjugates in an efficient and timely manner. As a lab-based role, this person will assist in the implementation and use of scientific and analytical equipment to yield high-quality conjugate materials.

Specific responsibilities for the Scientist, Conjugation Chemistry include:

  • Define and implement reproducible technical protocols to develop oligonucleotide conjugates for biological evaluation in our targeted delivery platform
  • Develop conjugation strategies (cysteine, lysine, glycan, site-specific, etc.) to yield stable and well-characterized oligonucleotide conjugates
  • Design and incorporate linker chemistries for oligonucleotide conjugates to optimize PKPD properties
  • Assist in internal lab build, procuring and utilizing equipment to enable conjugation and purification of antibody/peptide-oligonucleotide conjugates
  • Assist analytical scientists in developing methods (HPLC, MS, etc.) to characterize oligonucleotide conjugates
  • Work hand-in-hand with protein engineers and biologists to ensure timely and adequate preparation of oligonucleotide conjugates for biological evaluation as well as contribute to the design of in vitro and in vivo studies
  • Contribute to intellectual property around oligonucleotide-conjugates for the company

The Scientist, Conjugation Chemistry should be a doer with the ability to generate high-quality conjugate materials efficiently and effectively, while contributing to the interpretation of complex scientific data. This person should have direct experience working on antibody, protein, or peptide-based conjugation platforms with a significant background in chemistry and/or protein engineering. This person must demonstrate strong technical skills, taking novel ideas from paper and executing to turn them into rigorous and demonstrable results.

Key qualifications for the Scientist, Conjugation Chemistry include:

  • A degree (BS/MS/PhD) in chemistry, protein engineering, or a related discipline with 3+ years of experience working with antibody, protein, or peptide conjugates in the biopharmaceutical industry; title will be commensurate with level of qualifications and experience
  • Experience working with oligonucleotide-based therapeutic modalities such as siRNAs and ASOs is a plus
  • Adept in state-of-the-art conjugation (cysteine-maleimide, click chemistry, site-specific, etc.), purification (HPLC, SEC, IEX, etc.), and analytical (HPLC, LCMS, etc.) methods to prepare oligonucleotide conjugates
  • While demonstrating creativity to contribute to the development of novel delivery systems, this individual must also be process- and detail-oriented to ensure production of high-quality oligonucleotide conjugates
  • Imperative that this individual be an effective communicator and proven team-player, with the ability to operate independently in a laboratory setting

At a personal level, we are seeking an individual who is highly collaborative, intellectually curious, driven, trustworthy, humble, and who brings an adaptable and flexible working style. The Scientist, Conjugation Chemistry must be highly organized, thoughtful, and bring sound judgement and technical decision-making abilities. The company is creating a culture of highly engaged colleagues who put the team and the science above the self and operate with a sense of urgency. As such, the Scientist, Conjugation Chemistry should be highly nuanced in terms of their interpersonal style and able to lead and work effectively within a highly collaborative, entrepreneurial, and fast-paced start-up environment.

From an educational perspective, we are seeking an individual with a Ph.D. and/or BS/MS in a relevant discipline such as chemistry or protein engineering. It is understood that education, while an important index of achievement, orientation, and intellectual capacity, will not constitute the primary variable in this decision process. Personal characteristics, leadership abilities, technical fluency, creativity, work ethic, behavioral flexibility, and demonstrated accomplishments will serve as key components in the evaluation of candidates. This person will be based on-site at the company's headquarters in Cambridge, MA.