AI/ML Engineer
Therapeutic Protein Design
Posted on 9/29/2023
Ginkgo Bioworks

1,001-5,000 employees

Engineering biology for diverse commercial applications.
Company Overview
Ginkgo Bioworks, Inc. stands out as a leading bioengineering company that leverages advanced biological manufacturing technology to design and optimize a wide range of commercial products, from vaccines to sustainable fashion materials. The company's commitment to diversity, equity, and inclusion (DEI) fosters a unique and inclusive culture, promoting a diverse workforce that contributes to its success. Furthermore, Ginkgo's ability to engineer biology for equitable distribution of benefits positions it as a key player in various industries, including healthcare, agriculture, and fashion.
Consumer Goods
Food & Agriculture

Company Stage


Total Funding





Boston, Massachusetts

Growth & Insights

6 month growth


1 year growth


2 year growth

Canton, MA, USA
Experience Level
Desired Skills
Data Structures & Algorithms
Data Analysis
AI & Machine Learning
  • PhD in bioengineering, computer science, biophysics, biochemistry, computational biology, bioinformatics, chemical engineering, or related field plus 3 years experience. May include post doctoral or industry experience. Masters plus 5 years additional postgraduate or industry relevant experience
  • Hands-on experience (5+ years) in protein design and engineering, with a deep understanding of developability considerations for therapeutic proteins
  • Hands-on experience (2+ years) in developing and applying machine learning and AI algorithms for protein design
  • Broad knowledge of state-of-art machine learning approaches to protein design and biological data analysis. Familiarity with recent literature and state of the art for large model architectures and training approaches
  • Fluency with Python. Knowledge of best practices for software development, including version control, code reviews, unit testing, and continuous integration
  • Strong communication skills, both written and verbal, for effective collaboration within interdisciplinary teams
  • Enthusiasm to learn new techniques. Strong curiosity of areas of biology previously unknown to you
  • Ability to work independently, manage multiple projects, and meet project timelines
  • Protein Design and Engineering: Lead and contribute to the design and engineering of therapeutic proteins, focusing on enhancing developability attributes such as solubility, stability, prolonged half-life in serum, formulation considerations, and mitigating immunogenicity through computational methods
  • Machine Learning and AI Integration: Develop and implement machine learning and AI algorithms to predict and optimize protein properties, allowing for the creation of highly effective and safe therapeutic proteins
  • Immunogenicity Mitigation: Apply deep knowledge of immunogenicity mechanisms to design strategies that effectively mitigate immunogenic responses in therapeutic proteins, ensuring their safety and efficacy
  • Data Analysis: Analyze extensive biological datasets to extract insights into protein engineering and developability, informing decision-making processes in therapeutic protein development
  • Collaboration: Collaborate closely with interdisciplinary teams of scientists, including biochemists, mammalian biological engineers, and other protein designers to translate computational insights into practical therapeutic solutions
  • Research and Development: Stay updated with the latest advancements in protein design, machine learning, and AI through active participation in scientific literature review and attendance at relevant conferences
  • Influence the roadmap for AI at Ginkgo: Identify opportunities for application of AI and ML across the company, create prototypes, and contribute to overall prioritization and roadmap development for AI at Ginkgo
  • Take part in something big: This is a growing team, a significant company focus, and a rapidly evolving field. You will be able to influence where things go and how they change
Desired Qualifications
  • Strong publication record in protein design and engineering for therapeutic protein applications
  • 4+ years experience in applying protein design to any application within protein binder engineering, bispecific antibody design, CAR-T / cell therapy applications, gene editors, or capsid engineering
  • Knowledge and hands-on experience with physics-based protein modeling and design methods are a plus. Familiarity with at least one type of molecular modeling software such as PyMOL, Rosetta, Schrodinger, Molecular Operating Environment (MOE) a plus. Expertise in the computational modeling of biomacromolecules is a plus
  • Hand-on wet-lab experience in protein sciences or experience working closely with experimentalists strongly preferred