Team Introduction

The Protein Engineering Team works to address the complex challenges of protein and enzyme discovery, optimization, and design. We develop, onboard, stress-test, and utilize state-of-the-art protein discovery and design techniques in a continuously improving suite of AI, machine learning, and computational protein design tools. We are responsible for building a platform to “make proteins easier to engineer”, and deliver on protein design challenges that span a range of applications from health, agriculture, commodity chemicals, materials, flavors and fragrances, and more. 

Ginkgo recently announced a large partnership with Google Cloud to build a generative AI platform for engineering biology and for biosecurity. The Protein Engineering team is responsible for delivering best-in-class foundational models and application-specific models to tackle a range of protein design challenges, from generative models for design of enzyme sequences with novel catalytic functions to developing models for significantly accelerating the development of therapeutic proteins. 

Specific Role Description

As a Therapeutic Protein Engineer at Ginkgo Bioworks, you will play a vital role in advancing our efforts to engineer and optimize therapeutic proteins for diverse applications. Your expertise in protein design, coupled with your proficiency in machine learning and AI, will enable you to drive the development of novel therapeutic proteins with improved or novel functional characteristics in addition to engineering for developability properties such as solubility, stability, and reduced immunogenicity. 

You will leverage Ginkgo’s wealth of proprietary protein data to design, build, and train novel machine learning and AI models for application to protein design and optimization. We have access to nearly limitless compute capacity: CPU, GPU, or TPU. In addition, you will have access to Ginkgo’s experimental platform and resulting large datasets for generating and testing hypotheses using machine learning approaches as well as informing strategic training data acquisition.

Responsibilities

• 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.

Minimum Requirements

• 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

Preferred Capabilities and Experience

• 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

Total compensation for this role is market driven, with a starting salary of $110K +, as well as company stock awards.  Base pay is ultimately determined based on a candidate’s skills, expertise, and experience.  We also offer a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, Employee Assistance Program, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.