ZipRecruiter

Log In

1

Protein Engineering Scientist Jobs (NOW HIRING)

Manifold Bio

Scientist, cDNA Display

Boston, MA · On-site

$118K - $138K/yr

Our team of protein engineers, biologists, and computational scientists works across this full stack to pursue programs both internally and with leading pharma companies. Position Manifold Bio is ...

next page

Showing results 1-20

People also search for

All JobsProtein Engineering Scientist Jobs

Protein Engineering Scientist information

See salary details

$40.5K

$98.8K

$156.5K

How much do protein engineering scientist jobs pay per year?

As of Jun 7, 2026, the average yearly pay for protein engineering scientist in the United States is $98,759.00, according to ZipRecruiter salary data. Most workers in this role earn between $78,000.00 and $116,000.00 per year, depending on experience, location, and employer.

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

To thrive as a Protein Engineering Scientist, you need a strong background in molecular biology, biochemistry, and protein design, typically demonstrated through an advanced degree (MSc or PhD) in a life science field. Experience with techniques such as site-directed mutagenesis, protein expression and purification, and familiarity with analytical tools like HPLC, mass spectrometry, and relevant bioinformatics software is essential. Strong problem-solving abilities, attention to detail, and effective teamwork and communication skills set top candidates apart. Mastery of these areas is crucial for efficiently designing, optimizing, and characterizing proteins that meet organizational and research goals.

What are some typical day-to-day responsibilities for a Protein Engineering Scientist?

As a Protein Engineering Scientist, your daily responsibilities often include designing and executing experiments to modify protein structures, analyzing biochemical data, and troubleshooting experimental results. You’ll regularly use both laboratory techniques and computational tools to optimize protein properties, document your findings, and present data to project teams. Collaboration is a key part of the role, so you’ll frequently interact with colleagues from molecular biology, bioinformatics, and downstream process development groups. This dynamic environment keeps the work intellectually stimulating and offers ongoing opportunities to learn from multidisciplinary teams.

What is a Protein Engineering Scientist job?

A Protein Engineering Scientist designs and optimizes proteins for specific applications using techniques like directed evolution and computational modeling. They work in biotechnology, pharmaceuticals, or academic research to develop enzymes, antibodies, or therapeutic proteins. Their role includes molecular biology, structural analysis, and laboratory experimentation to improve protein function, stability, or specificity.

More about Protein Engineering Scientist jobs
What cities are hiring for Protein Engineering Scientist jobs? Cities with the most Protein Engineering Scientist job openings:
What are the most commonly searched types of Protein Engineering Scientist jobs? The most popular types of Protein Engineering Scientist jobs are:
What states have the most Protein Engineering Scientist jobs? States with the most job openings for Protein Engineering Scientist jobs include:
What job categories do people searching Protein Engineering Scientist jobs look for? The top searched job categories for Protein Engineering Scientist jobs are:
Protein Engineering Scientist jobs near you
Scientist / Senior Scientist, Protein Engineering

Scientist / Senior Scientist, Protein Engineering

Kodiak Sciences Inc.

Palo Alto, CA

$105K - $143K/yr

Full-time

Posted 25 days ago

Job description

Kodiak Sciences Inc. is a fast-growing, clinical-stage biopharmaceutical company focused on transforming ophthalmology through innovative therapeutics. Our Antibody Biopolymer Conjugate Drug (ABCD) platform integrates protein and peptide engineering & discovery, polymer chemistry, small molecule drug discovery, bioconjugation, and drug delivery technologies to address high-prevalence ophthalmic diseases.
We are seeking a talented Scientist/Senior Scientist to advance peptide therapeutic drug discovery and development programs with a strong emphasis on molecular design, organic synthesis, and analytical characterization.
Key Responsibilities
  • Lead the design, synthesis, and optimization of peptide-based therapeutics, integrating Structure-Activity Relationship (SAR) considerations, developability and conjugation strategies to drive candidate progression.
  • Perform hands-on experimental work including, but not limited to DNA-Encoded Library synthesis, Macrocyclic and Linear Peptide synthesis, polymer conjugation chemistry, purification and analytical evaluation, data interpretation and developability risk assessment.
  • Develop and apply analytical and biophysical methods (e.g., LC-MS, HPLC, NMR, SEC, DLS) to characterize peptides and bioconjugates, including purity, heterogeneity, stability, and aggregation.
  • Collaborate cross-functionally and communicate scientific findings through presentations, reports, and regulatory documentation.
Education / Qualifications
  • Ph.D. in Medicinal Chemistry, Organic Chemistry, Chemical Biology, Biochemistry, or a related field, with either (i) 0–3 years of relevant postdoctoral experience and at least one first-author publication in a high-impact, peer-reviewed journal (preferred), or (ii) 3+ years of relevant industry experience.
  • Experience working with either of the following methodologies, such as Solid Phase Peptide Synthesis (SPPS), DNA-Encoded Library (DEL) synthesis, liquid phase parallel synthesis and/or polymer-based bioconjugates is highly desirable.
  • Strong experience in therapeutic development of peptides, and/or conjugated biologics, experience in analytical characterization is a plus.
  • Proficiency in chromatographic and mass spectrometry-based techniques, with an understanding of developability attributes such as stability, solubility, and manufacturability is a plus.
  • Experience in using software such as PyMol, MOE, Schrödinger, Maestro, DataWarrior, Vortex is a plus.
  • Experience with CD and/or FTIR for peptide secondary structure determination is a plus.
  • Hands-on experience with biochemical assays, including SPR, ELISA, fluorescence-based assays, is a plus.
  • Demonstrated ability to independently drive scientific work in a collaborative, cross-functional environment, with strong problem-solving and communication skills.