(Senior) Scientist, Protein Design

About Abiologics

Abiologics is a Flagship Pioneering company developing Synteins™ - a transformative class of fully synthetic proteins composed entirely of artificial building blocks such as D-amino acids and non-canonical residues. SynteinsTM are designed to transcend the limitations of traditional biologics, with improved oral stability, immune evasion, and metabolic durability - all while being fully programmable by design.

Powered by a proprietary AI-enabled discovery platform, Abiologics integrates generative design , automated synthesis , and rapid experimental screening to enable iterative optimization at scale.

Position Summary

We are seeking a Protein Design Scientist to drive the structure-based design and optimization of synthetic proteins. This is a highly interdisciplinary role at the interface of computational design, structural biology, and protein engineering.

Ideal candidates have deep experience in de novo protein design , miniproteins , and binder engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment.

Key Responsibilities

• Design and execute SynteinsTM engineering campaigns to generate drug candidates
• Create computational design strategies to deliver drug candidates drawing from array of ML tools and Rosetta scripts
• Collaborate with computation, chemistry, and experimental biology teams to optimize designs for function, solubility, and stability
• Integrate structural and biophysical data (e.g., BLI binding, CD, HDX-MS, CryoEM) into iterative optimization cycles

Qualifications

Required

• PhD in structural biology, biophysics, protein design, or related field
• 2+ years of hands-on experience in structure-guided protein design
• Demonstrated proficiency with modern structure prediction and design tools such as RFdiffusion, proteinMPNN, AF2, ESMFold, Boltz, Rosetta or equivalent SOTA tools for in-silico protein engineering
• Strong understanding of the biophysics of protein folding and interface energetics
• Demonstrated ability to progress designs from concept to experimental testing
• Excellent communication skills

Preferred

• Experience designing minibinders or proteins <100 AAs
• Familiarity with non-canonical amino acid design
• Familiarity with molecular dynamics tools
• Exposure to high-throughput or automated protein engineering environments
• Prior work on platform-based or early-stage biotech teams

Why Join Abiologics

• Help invent a new class of programmable synthetic proteins
• Be part of a high-velocity discovery platform with real-time synthesis and screening
• Collaborate with a deeply interdisciplinary, mission-driven team
• Redefine the limits of what proteins can do

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.

About Flagship Pioneering:

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health and sustainability exponentially accelerate scientific progress in areas ranging from cancer detection and treatment to nature-positive agriculture. What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. 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.

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.