What if… you could join an organization that is discovering and developing an entirely new class of medicines, one that leverages both chemistry and biology, to overcome many of the challenges faced by current therapeutics today?

Company Summary:

Flagship Labs 83, Inc. (FL83) is a privately held, early-stage biotechnology company on a mission to make biology better through chemistry. We are pioneering the development of a transformational new class of medicines, called Artificial Biologics™, that is unlocked by novel synthetic and computational technologies. We seek an exceptional Computational Scientist to join our entrepreneurial and innovation-driven organization.

FL83 was founded in Flagship Pioneering’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA) and Generate Biomedicines were conceived and created. Since Flagship’s founding in 2000, the firm has originated and fostered the development of more than 100 scientific ventures resulting in over $34 billion in aggregate value, more than 500 issued patents and more than 50 clinical trials for novel therapeutic agents.

Position Summary:

Flagship Labs 83 is looking for a creative and motivated Computational Protein Design Scientist or Senior Scientist to establish our Artificial Biologics Computational Protein Design team. As part of the early scientific team, this individual will be instrumental in building the Computational Protein Design platform, using data-driven approaches to tackle Artificial Biologics design challenges and develop impactful new medicines. The ideal candidate will have experience applying state-of-the-art machine learning and computational methods to design novel peptides and proteins such as structure modeling and prediction, structure library generation, molecular docking, and multiparameter molecular property optimization.  A successful candidate will be an excellent collaborator working closely with our Platform Development and Biology teams to implement and execute rapid design-build-test cycles and optimized methods.


  • Develop and implement a novel computational design platform for predicting the properties of peptides, proteins, and unnatural biopolymers using state-of-the-art computational modeling and machine learning approaches
  • Design new macromolecular therapeutics using rational protein engineering methods, and employ these in silico predictions to iteratively guide the experimental chemistry team
  • Discover new sequence/structure-function relationships and macromolecular design principles by leveraging large experimental datasets and streamlining their analysis
  • Analyze, interpret, document and present data to scientific and leadership team
  • Contribute to ongoing innovation within the company through the introduction of the most recent trends in machine learning and computational protein design
  • Maintain a broad awareness of the developments in computational drug design
  • Work closely with Platform Development and Biology teams to integrate a tight design-build-test cycle leveraging FL83’s proprietary technology
  • Work within an entrepreneurial, collaborative, and interdisciplinary team to actively contribute to creating, shaping, and executing the vision of the company


  • PhD (or equivalent) in computational biology, computational chemistry, bioengineering, biophysics, or a related field
  • 3+ years of experience developing computational and/or machine learning methods to solve problems related to peptide and protein design, modeling, and sequence/structure-function prediction
  • Proficient in Python and significant experience with relevant macromolecular modeling software (i.e. AlphaFold, ESM, PyRosetta, MOE, Schrödinger)
  • Familiar with deep learning libraries (i.e. PyTorch)
  • Experience with cloud computing (i.e. AWS) and software is a plus

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.

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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