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Protein Design Jobs in Ontario (NOW HIRING)

Manifold Bio

CA$140K - CA$225K/yr

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of ...

Maple Leaf Foods

Reliability Engineer

Hamilton, ON

CA$71K - CA$103K/yr

Incremental HeadcountCompensation:???$71,000 - $103,000 CAD base pay annually plus annual short ... protein company on earth, and a deep commitment to sustainable protein across North America.An ...

Maple Leaf Foods

FSQA Process Leader

Hamilton, ON

CA$47K - CA$69K/yr

Existing HeadcountBase Salary:? ?$47,000 - $69,000 CAD base pay annuallyThe above base salary ... protein company on earth, and a deep commitment to sustainable protein across North America.An ...

Maple Leaf Foods

Sourcing Buyer

Mississauga, ON

CA$71K - CA$103K/yr

Compensation:??$71,000 - $103,000 CAD base pay annually plus annual short-term incentive?The above ... protein company on earth, and a deep commitment to sustainable protein across North America.An ...

BinSentry

Electronic Assembler

Kitchener, ON · On-site

CA$18.50 - CA$19.50/hr

With our technology, feed mills, commercial grain handling facilities, and protein producers are ... We handle the design, manufacturing, and assembly of our own hardware, with a strong emphasis on ...

BinSentry

Electronic Assembler

Kitchener, ON · On-site

$18.50 - $19.50/hr

With our technology, feed mills, commercial grain handling facilities, and protein producers are ... We handle the design, manufacturing, and assembly of our own hardware, with a strong emphasis on ...

BinSentry

Product Manager

Kitchener, ON · On-site

With our technology, feed mills, commercial grain handling facilities, and protein producers are ... Coordinate and drive the design, prototyping, revision, certification, and productization and NPI ...

BinSentry

Senior Embedded Software Developer

Kitchener, ON · On-site

CA$125K - CA$165K/yr

With our technology, feed mills and protein producers are enhancing feed ordering efficiency ... The ideal candidate will design, develop, and maintain software for embedded systems, working ...

Tofurky

Senior Food Scientist (61026)

Hood River, OR · On-site

... protein and dairy-free cheese products. Reporting to the VP of R&D, this role owns projects from ... Design and execute product quality and stability experiments; analyze and interpret data to make ...

Cargill

Fsqr Labourer-Afternoons - Jarvis

Jarvis, ON · On-site

CA$27.09/hr

... protein, salt, oils, starches, sweeteners, cocoa and chocolate. Job Purpose and Impact Type : Full Time Shift(s) Available : Afternoon Pay Rate: $27.09 CAD/hr This job posting is for an existing ...

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All JobsProtein Design JobsProtein Design Jobs in Ontario

Protein Design information

What is protein design?

Protein design is the process of creating new proteins or modifying existing ones to have specific functions or properties. This can involve using computational tools, laboratory techniques, or a combination of both to predict and engineer amino acid sequences that will fold into desired three-dimensional structures. Protein design is used in various fields, including medicine, biotechnology, and research, to develop novel enzymes, therapeutics, or materials. The field requires a strong understanding of biology, chemistry, and computer science to achieve successful outcomes.

What are the key skills and qualifications needed to thrive as a protein design scientist, and why are they important?

To thrive as a Protein Design Scientist, you need a strong background in molecular biology, biochemistry, and computational modeling, typically supported by an advanced degree in a relevant field. Proficiency with tools such as Rosetta, PyMOL, and molecular dynamics simulation software, as well as experience with protein expression and purification techniques, is essential. Analytical thinking, problem-solving, and effective communication are important soft skills to drive innovation and collaborate with interdisciplinary teams. These skills are crucial for designing functional proteins, troubleshooting experiments, and advancing research goals in biotechnology and pharmaceutical development.

What are some typical challenges faced by professionals in protein design, and how are they addressed within a team setting?

Professionals in protein design often encounter challenges such as predicting accurate protein folding, ensuring stability, and achieving desired biological activity. These complexities are typically addressed through close collaboration with computational biologists, structural biologists, and experimental scientists. Teams frequently hold cross-functional meetings to troubleshoot issues, share findings, and iterate on design strategies based on laboratory results. This collaborative environment helps leverage diverse expertise and accelerates the development of novel proteins with desired functions.

What is the difference between Protein Design vs Protein Engineering?

AspectProtein DesignProtein Engineering
Required CredentialsBiochemistry, Molecular Biology, BioinformaticsBiochemistry, Molecular Biology, Bioinformatics
Work EnvironmentResearch labs, biotech companies, academiaResearch labs, biotech companies, academia
Industry UsageDesigning novel proteins, drug development, synthetic biologyModifying existing proteins for improved function or stability

Protein Design focuses on creating new proteins with specific functions, often using computational methods. Protein Engineering involves modifying existing proteins to enhance or alter their properties. Both roles require similar skills and are used in research, biotech, and pharmaceutical industries, but their goals differ: one designs from scratch, the other optimizes existing proteins.

What are popular job titles related to Protein Design jobs in Ontario?

For Protein Design jobs in Ontario, the most frequently searched job titles are:

What job categories do people searching Protein Design jobs in Ontario look for?

The top searched job categories for Protein Design jobs in Ontario are:

Protein Design jobs near you
Infographic showing various Protein Design job openings in Ontario as of August 2026, with employment types broken down into 82% Full Time, 15% Part Time, and 3% Contract. Highlights an 85% Physical, 4% Hybrid, and 11% Remote job distribution.

AI/ML Research Engineer

On-site

Manifold Bio
Biotechnology Research and Development • 1 - 10 employees
Learn more about Manifold Bioexternal

CA$140K - CA$225K/yr

Full-time

Medical, Dental, Vision, Retirement, PTO

Re-posted 10 days ago

Job description

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of living systems. Using proprietary molecular barcoding technology, we screen hundreds of thousands of protein designs simultaneously in living systems, producing in vivo-validated datasets at a scale no one else can match. The datasets power our computational models, which leads to better drug designs, creating a flywheel that gets stronger with every campaign. 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 seeking a talented Machine Learning Research Engineer to join our growing AI team. You will work closely with our research scientists to implement, scale, and optimize machine learning systems that power our de novo antibody design platform and advance our protein design capabilities. Your efforts will contribute to building production-ready ML infrastructure that enables breakthrough discoveries in protein therapeutics. You will be expected to take ownership of engineering challenges in our ML pipeline, from data processing and model training to deployment and monitoring, while collaborating closely with our research team to translate cutting-edge ideas into robust, scalable systems.

This is an on-site role and can be based in either Boston, Massachusetts or San Francisco, California. Please only apply if you reside in these cities or are open to relocate. 

Responsibilities

  • Implement and optimize machine learning models for protein design
  • Build and maintain scalable data processing pipelines for large-scale protein and molecular datasets
  • Develop and deploy ML infrastructure for distributed training and inference across GPU clusters
  • Collaborate with research scientists to translate experimental ML approaches into production-ready code
  • Design and execute ML experiments with clear hypotheses and rigorous analysis
  • Optimize model performance and computational efficiency for large-scale protein design tasks
  • Build tools and utilities to support rapid prototyping and experimentation by the research team

Required Qualifications

  • Bachelor's or Master's degree in Computer Science, Machine Learning, Computational Biology, or related field
  • 2+ years of hands-on experience with PyTorch and/or JAX for deep learning applications
  • Strong proficiency in Python scientific computing stack (NumPy, Pandas, scikit-learn)
  • Experience with distributed computing and GPU optimization techniques
  • Familiarity with protein structure analysis, computational biology, or analogous problems in natural sciences
  • Understanding of modern deep learning architectures and optimization techniques
  • Experience implementing research papers or translating ML approaches to production systems
  • Proficiency with version control (Git), testing frameworks, and software engineering best practices
  • Strong problem-solving skills and ability to work independently on technical challenges
  • Excellent written and verbal communication skills for cross-functional collaboration

Preferred Qualifications

  • Experience training LLMs or diffusion generative models
  • Knowledge of cloud computing platforms (AWS, GCP) and containerization (Docker, Kubernetes)
  • Background in computational biology, bioinformatics, or structural biology
  • Experience with large-scale data engineering and ETL pipelines
  • Familiarity with MLOps practices and model deployment frameworks

This Role Might Be Perfect For You If

You are passionate about leveraging state of the art machine learning approaches to solve challenging disease areas

  • You enjoy translating research ideas into high impact, productionized, scalable code
  • You have rich AI/ML experience and are looking to pivot into biotech

If you're excited to build scalable ML systems that revolutionize protein therapeutic discovery, please reach out to careers@manifold.bio.

Base Salary Range: $140,000-225,000

This reflects the typical offer range for this role, based on experience, role scope, and internal equity. Final compensation decisions are made using a consistent leveling framework and consider the candidate's experience, interview performance, and expected impact.

This role is eligible for:

  • Annual performance-based target bonus
  • Stock options
  • Comprehensive medical, dental, and vision coverage
  • 401(k) plan
  • Flexible paid time off and holidays
  • Perks including on-site gym, onsite lunch, and commuter support

Our compensation ranges are reviewed annually to ensure alignment with market trends and internal equity.

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