Company Summary:

FL89, Inc. is a privately held early-stage company that is leveraging advanced biological and computational tools to develop breakthroughs in our understanding of secreted protein function and regulation in human physiology. More specifically, FL89 is pairing high throughput -omics technology with AI/ML based protein structure prediction to define and discover novel therapeutic protein biology.

Flagship Pioneering has conceived of and created companies such as Moderna Therapeutics (NASDAQ: MRNA), Editas Medicine (NASDAQ: EDIT), Omega Therapeutics (NASDAQ: OMGA), Seres Therapeutics (NASDAQ: MCRB), and Indigo Agriculture. Since its launch in 2000, Flagship has applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures. In 2021, Flagship Pioneering was ranked 12th globally 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.

Position Summary:

We are seeking an energetic and motivated scientist with extensive experience in computational structural biology and developing AI/ML models for generative protein design to join our tight-knit team. The ideal candidate has superior skills in these areas, particularly as it pertains to the interplay between protein sequence, structure, and high-dimensional NGS assays, and thrives in a fast-paced and collaborative startup environment. The position will provide a unique opportunity to play a critical role in the advancement of FL89’s computational discovery and preclinical platforms, through the development of disruptive approaches for biotherapeutic drug discovery.

The candidate will apply computational models to better understand and describe protein structure-function rules that impact human health. The candidate will design and implement novel approaches to modeling protein structure, develop structural alignment tools, assign functional similarities, and work with the experimental teams to build a reiterative learning loop to identify, classify, and validate novel secreted proteins and protein functions. An ideal candidate will pride themselves on their ability to craft scientifically logical stories out of complex structural data, develop AI/ML tools to describe key structural definitions that drive biological mechanisms, and leverage discoveries into viable biomarker or therapeutic targets.

Minimum Qualifications:

  • PhD in computational biology (or equivalent)
  • 3-5+ years of experience implementing AI/ML models for generative protein design
  • 5-7+ years of industry experience in computational structural biology or a related field such as computational evolutionary biology, or protein engineering
  • Demonstrated industry experience or academic achievement, as evidenced by publications in high impact journals, conference proceedings, or widely used codebase
  • Proficiency with bioinformatics tools in the protein space (e.g. AlphaFold, Rosetta, etc.)
  • Strong familiarity with topics of protein and macromolecular structures and interactions with other proteins
  • Experience in developing & deploying machine learning platforms using modern Python frameworks for deep learning (e.g. PyTorch)
  • Experience with cloud environments such as AWS
  • Knowledge of best practices in software engineering for reproducibility and data management skills
  • Ability to work in and adapt to a fast-paced environment

Preferred Qualifications:

  • Experience with protein co-evolution analysis
  • Experience with NGS and bioinformatics tools


Flagship Pioneering is 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.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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