Computational Protein Design Contractor

Who We Are

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 www.flagshippioneering.com.

Mission:

Design and optimize self-assembling protein monomers for in-vivo delivery, combining state-of-the-art structure prediction with practical design loops. 

This contract will likely be 200 hours to start.

Impact:

• Deliver de novo and variant sequences with structure predictions and clear design rationales. 
• Stand up an iterative design pipeline (models + DOE) that improves hit rate each cycle. 
• Hand off code, documentation, and concise review-ready summaries. 

Responsibilities:

• Analyze conserved motifs and assembly interfaces; propose stabilizing or functional mutations. 
• Run and interpret multimeric structure, immunogenicity, aggregation, and expression predictors. 
• Use Rosetta/PyRosetta, ProteinMPNN, RFdiffusion, and AlphaFold-Multimer and related tools in a disciplined design-make-test-learn loop, alongside associated immunogenicity tools (NetMHCpan) 

Qualifications:

• Track record designing self-assembling protein complexes or cages. 
• Proficiency with Rosetta/PyRosetta; ProteinMPNN; AlphaFold-Multimer; RFdiffusion (or equivalent). 
• Experience assessing immunogenicity (e.g., NetMHCpan/MHCflurry/IEDB), aggregation (e.g., CamSol/Aggrescan3D), and expression/solubility predictors. 
• Strong Python; reproducible research (conda/Poetry, Docker, Git). 
• Clear technical communication; disciplined experiment planning (DOE). 

Nice-To-Haves

• Active-learning or Bayesian optimization for sequence design; design space coverage analysis. 
• Foldseek, ESMFold/ESM-IF, RosettaScripts, task-aware scoring customization. 
• Basic immunology of T-cell epitopes and de-immunization strategies. 
• Experience supporting IP filings (computational evidence packs). 

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 www.flagshippioneering.com.

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 perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.