Computational Protein Design Contractor

ABOUT PIONEERING INTELLIGENCE

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

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. 

KEY 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) 

PROFESSIONAL EXPERIENCE & 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 PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

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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