Principal Scientist, Computational Protein Design

Pioneering Intelligence is a strategic initiative of Flagship Pioneering committed to positioning Flagship at the forefront of global prosperity through the synthesis of human, machine, and nature’s intelligence -- which we call Polyintelligence. Pioneering Intelligence is seeking a Principal Scientist – Computational Protein Design to serve as the technical lead on computational antibody design efforts pushing the forefront of AI-based antibody design approaches on high value targets.

This position will be in collaboration with Pioneering Medicines, Flagship Pioneering’s initiative building a world-class biopharmaceutical R&D capability harnessing the power of Flagship’s scientific platforms.

Position Summary

As Principal Scientist – Computational Protein Design
, you will lead technical development in computational antibody design and develop ability optimization, playing a pivotal role in advancing our AI-based design methods to build new foundational workflows for end-to-end antibody design, and apply those workflows to advance new medicines in collaboration with Pioneering Medicines. The ideal candidate will combine strong scientific and computational know-how with proficiency in working within highly matrixed, cross-functional team environments.

Join us to shape the future of cutting-edge antibody therapeutics across Flagship’s portfolio of technology platforms.

Key Responsibilities

• Design and optimize antibodies using AI-based and structure-based approaches for binding and functionality.
• Create and apply computational methods for assessing and optimizing develop ability (stability, solubility, manufacturability, immunogenicity, polyreactivity, polyspecificity).
• Improve AI models with experimentally generated data.
• Stay at the forefront of AI and computational tools in antibody engineering.
• Provide scientific leadership and mentor team members.

Required Qualifications

• PhD in Biochemistry, Structural Biology, Biophysics, Protein Engineering, Computational Biology, Computer Science, or related field with 5+ years of relevant industry experience.
• Proven experience in the end-to-end design and optimization of antibodies for binding, functionality, and develop ability.
• Strong track record in utilizing AI and computational methods for antibody engineering, including but not limited to AI-based co-folding models and design models, and related structure-based design tools.
• Experience analyzing and interpreting antibody develop ability data.
• Experience leading projects in antibody discovery or biologics development.

Preferred Qualifications

• Expertise in a breadth of antibody modalities, including mAbs, bispecifics or multispecifics, antibody-drug conjugates (ADCs), and antibody fragments.
• Experience developing and training novel AI and machine learning models for protein engineering utilizing deep learning architectures.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no…