Senior Scientist - Protein Design and Engineering
About Us
Monod Bio is a pioneer company in the design of de novo protein reagents for Life Sciences and Diagnostics. Our innovative design platform technology takes advantage of the most recent advances in deep learning computational protein engineering to create highly rapid and sensitive protein-based reagents and assays. Our visionary founding team and state-of-the-art technology and product development experience position Monod Bio at the forefront of molecular reporter, binder and functional protein innovation, and we welcome exceptional individuals to join us in this journey.
About the Role
We are currently seeking a Senior Scientist - Protein Design and Engineering to help us lead the development of next-generation de novo protein reagents. This individual will drive protein design efforts from concept through implementation, working closely with a multidisciplinary team of computational designers, assay developers, and protein engineers. The ideal candidate will have deep expertise in molecular biology, protein engineering, and biophysical characterization, along with a track record of success developing novel protein-based technologies.
Key Responsibilities
Lead the design, screening, and characterization of de novo protein reagents across a range of applications, from conceptualization through downstream implementation and validation.
Design and execute protein engineering / directed evolution campaigns strategies-including structure-guided design, directed evolution, and mutagenesis workflows-to improve target binding affinity, stability, and selectivity.
Collaborate cross-functionally to align project objectives, timelines, and design needs with downstream applications.
Guide the development and screening of DNA libraries using yeast surface display or other display technologies (e.g., phage), including FACS-based selection and flow cytometry analysis.
Oversee molecular biology workflows including cloning, site-directed mutagenesis, and high-throughput construct assembly.
Characterize designed proteins using biophysical and biochemical techniques, including binding kinetics (SPR, BLI), thermal stability (DSF/SLS), and secondary structure (CD).
Contribute to data analysis and interpretation, clearly communicating findings and recommendations to internal teams.
Maintain detailed experimental records in Benchling and contribute to documentation for internal and external reporting.
Stay current with advancements in protein design and engineering, bringing new ideas and techniques into the team.
Required Qualifications
D. in molecular biology, biochemistry, bioengineering, or a related field, with 3+ years of relevant industry experience.
Proven track record in protein engineering, including structure-guided design, de novo design, and/or antibody/protein scaffold engineering.
Strong molecular biology skills, including PCR, cloning, Golden Gate or Gibson assembly, and SSM/EP-PCR mutagenesis.
Hands-on experience with protein expression and purification (primarily E. coli), including NiNTA, StrepTactin, and size exclusion chromatography.
Proficiency in biophysical and analytical methods: SPR/BLI, CD, SEC-MALS, DSF, SDS-PAGE, and Western blotting.
Highly qualified in high-throughput screening and display-based selection platforms (yeast, phage, or ribosome display).
Strong understanding of the biophysics of protein structure/function relationships and confidence with structure modeling and visualization tools (e.g., PyMOL, Chimera, AlphaFold). A huge plus is demonstrated proficiency in protein modeling and design using Protein MPNN, RFdiffusion or equivalent tools for insilico protein engineering.
Comfortable working in a fast-paced, interdisciplinary team; experience mentoring or managing others is a strong plus.
Strong communication skills and ability to present data and proposals to a range of audiences.
Physical environment and key requirements:
Ability to perform work in both an office and laboratory environment. Will be in proximity to BSL2 labs. Familiarity with biological and chemical hazard handling. Training and equipment will be provided, as necessary.
Office mobility and the ability to stand for periods of time as needed is required.
Operations happen in moderately loud environments. PPE included by the company.
Mild odors from the manufacture of physical specimens and from laboratory work. The environment has been tested, and proper engineering protections are in place.
We are proud to provide a generous benefits package and a healthy work culture:
Competitive salary plus bonus opportunity.
100% company-paid medical, dental, life/AD&D, and vision insurance premiums for employees scheduled to work 25+ hours per week. 50% paid premiums for eligible dependents.
4 weeks PTO per year plus 11 paid holidays.
Parental leave benefit.
Annual compensation reviews.
State-of-the-art lab and office on bus line and near coffee shops, restaurants, and South Lake Union neighborhood.
Casual environment, friendly colleagues, and of course, excellent snacks in the kitchen!
Every position requires certain physical capabilities with the major ones for this role noted above. Monod Bio seeks to provide reasonable accommodations that enable individuals with disabilities to perform essential duties when possible. Equal employment opportunity is a fundamental principle at Monod Bio. We are committed to nondiscrimination in all business operations. We are proud to enjoy a respectful and inclusive work environment where everyone has the opportunity to thrive.
Senior Scientist - Protein Design and Engineering
MonoDBio
Seattle, WA
Full Time
USD 120,000.00 - 150,000.00 per year
Published on 08/06/2025
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About Us
Monod Bio is a pioneer company in the design of de novo protein reagents for Life Sciences and Diagnostics. Our innovative design platform technology takes advantage of the most recent advances in deep learning computational protein engineering to create highly rapid and sensitive protein-based reagents and assays. Our visionary founding team and state-of-the-art technology and product development experience position Monod Bio at the forefront of molecular reporter, binder and functional protein innovation, and we welcome exceptional individuals to join us in this journey.
About the Role
We are currently seeking a Senior Scientist - Protein Design and Engineering to help us lead the development of next-generation de novo protein reagents. This individual will drive protein design efforts from concept through implementation, working closely with a multidisciplinary team of computational designers, assay developers, and protein engineers. The ideal candidate will have deep expertise in molecular biology, protein engineering, and biophysical characterization, along with a track record of success developing novel protein-based technologies.
Key Responsibilities
Lead the design, screening, and characterization of de novo protein reagents across a range of applications, from conceptualization through downstream implementation and validation.
Design and execute protein engineering / directed evolution campaigns strategies-including structure-guided design, directed evolution, and mutagenesis workflows-to improve target binding affinity, stability, and selectivity.
Collaborate cross-functionally to align project objectives, timelines, and design needs with downstream applications.
Guide the development and screening of DNA libraries using yeast surface display or other display technologies (e.g., phage), including FACS-based selection and flow cytometry analysis.
Oversee molecular biology workflows including cloning, site-directed mutagenesis, and high-throughput construct assembly.
Characterize designed proteins using biophysical and biochemical techniques, including binding kinetics (SPR, BLI), thermal stability (DSF/SLS), and secondary structure (CD).
Contribute to data analysis and interpretation, clearly communicating findings and recommendations to internal teams.
Maintain detailed experimental records in Benchling and contribute to documentation for internal and external reporting.
Stay current with advancements in protein design and engineering, bringing new ideas and techniques into the team.
Required Qualifications
D. in molecular biology, biochemistry, bioengineering, or a related field, with 3+ years of relevant industry experience.
Proven track record in protein engineering, including structure-guided design, de novo design, and/or antibody/protein scaffold engineering.
Strong molecular biology skills, including PCR, cloning, Golden Gate or Gibson assembly, and SSM/EP-PCR mutagenesis.
Hands-on experience with protein expression and purification (primarily E. coli), including NiNTA, StrepTactin, and size exclusion chromatography.
Proficiency in biophysical and analytical methods: SPR/BLI, CD, SEC-MALS, DSF, SDS-PAGE, and Western blotting.
Highly qualified in high-throughput screening and display-based selection platforms (yeast, phage, or ribosome display).
Strong understanding of the biophysics of protein structure/function relationships and confidence with structure modeling and visualization tools (e.g., PyMOL, Chimera, AlphaFold). A huge plus is demonstrated proficiency in protein modeling and design using Protein MPNN, RFdiffusion or equivalent tools for insilico protein engineering.
Comfortable working in a fast-paced, interdisciplinary team; experience mentoring or managing others is a strong plus.
Strong communication skills and ability to present data and proposals to a range of audiences.
Physical environment and key requirements:
Ability to perform work in both an office and laboratory environment. Will be in proximity to BSL2 labs. Familiarity with biological and chemical hazard handling. Training and equipment will be provided, as necessary.
Office mobility and the ability to stand for periods of time as needed is required.
Operations happen in moderately loud environments. PPE included by the company.
Mild odors from the manufacture of physical specimens and from laboratory work. The environment has been tested, and proper engineering protections are in place.
We are proud to provide a generous benefits package and a healthy work culture:
Competitive salary plus bonus opportunity.
100% company-paid medical, dental, life/AD&D, and vision insurance premiums for employees scheduled to work 25+ hours per week. 50% paid premiums for eligible dependents.
4 weeks PTO per year plus 11 paid holidays.
Parental leave benefit.
Annual compensation reviews.
State-of-the-art lab and office on bus line and near coffee shops, restaurants, and South Lake Union neighborhood.
Casual environment, friendly colleagues, and of course, excellent snacks in the kitchen!
Every position requires certain physical capabilities with the major ones for this role noted above. Monod Bio seeks to provide reasonable accommodations that enable individuals with disabilities to perform essential duties when possible. Equal employment opportunity is a fundamental principle at Monod Bio. We are committed to nondiscrimination in all business operations. We are proud to enjoy a respectful and inclusive work environment where everyone has the opportunity to thrive.
Senior Scientist - Protein Design and Engineering
MonoDBio
Seattle, WA
Full Time
USD 120,000.00 - 150,000.00 per year
Published on 08/06/2025
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Subscribe to Job Alerts
Job ID: 488983505
Originally Posted on: 8/11/2025
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