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Contract Protein Engineering Scientist Jobs (NOW HIRING)

Manifold Bio

Scientist, Cell-Free 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 ...

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Contract Protein Engineering Scientist information

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$40.5K

$98.8K

$156.5K

How much do contract protein engineering scientist jobs pay per year?

As of Jun 12, 2026, the average yearly pay for contract 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 Contract Protein Engineering Scientists?

Contract Protein Engineering Scientists are professionals who are hired on a temporary or project basis to design, modify, and optimize proteins for specific applications, such as pharmaceuticals, biotechnology, or research. They use techniques like directed evolution, rational design, and computational modeling to alter protein structures and functions to meet client needs. These scientists often work for contract research organizations (CROs), biotech companies, or as independent consultants, providing specialized expertise without long-term employment commitments.

What are some common challenges faced by Contract Protein Engineering Scientists when working with external clients?

Contract Protein Engineering Scientists often navigate complex project requirements and tight timelines set by external clients. Communication is key, as clients may have evolving goals or provide incomplete experimental data, requiring adaptability and frequent progress updates. Additionally, ensuring alignment on technical expectations and deliverables while maintaining scientific rigor can be challenging in a fast-paced, contract-based environment. Building strong collaborative relationships with both internal team members and client representatives helps overcome these hurdles and deliver successful project outcomes.

What are the key skills and qualifications needed to thrive as a Contract Protein Engineering Scientist, and why are they important?

To thrive as a Contract Protein Engineering Scientist, you need a strong background in molecular biology, biochemistry, and protein design, typically with a PhD or MSc in a related field. Experience with techniques such as site-directed mutagenesis, protein expression and purification, and familiarity with tools like PyMOL, Rosetta, and relevant bioinformatics databases is essential. Strong problem-solving abilities, attention to detail, and effective communication help you collaborate with cross-functional teams and manage project timelines. These skills and qualities are crucial for developing innovative protein solutions and ensuring project success in a fast-paced, contract-based environment.
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Contract Protein Engineering Scientist jobs near you
Infographic showing various Contract Protein Engineering Scientist job openings in the United States as of June 2026, with employment types broken down into 3% As Needed, 7% Full Time, 80% Part Time, 2% Temporary, and 8% Contract. Highlights an 80% Physical, 2% Hybrid, and 18% Remote job distribution, with an average salary of $98,759 per year, or $47.5 per hour.
Scientist / Senior Scientist, Protein Engineering

Scientist / Senior Scientist, Protein Engineering

Kodiak Sciences Inc.

Palo Alto, CA

$105K - $143K/yr

Full-time

Posted 29 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.