Senior Scientist, Computational Protein Design Boston, MA

Senior Scientist, Computational Protein Design

About Abiologics

Abiologicsis 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.

Synteins TM 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,Abiologicsintegrates generative design ,
automated synthesis , and rapid experimental screening to enable iterative optimization at scale.

Position Summary

We are seeking a Protein Design Scientist to join the Computational Protein Design team and help drive 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
, mini proteins
, and binders engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment.

• Design and execute Synteins TM 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., binding, CD, HDX-MS,CryoEM) into iterative optimization cycles

Required

• PhD in structural biology, biophysics, protein design, or related field
• 2+ years of hands‑on experience in structure‑guided protein design
• Demonstratedproficiencywith modern structure prediction and design tools such asRFdiffusion,protein
  
  MPNN, AF2, Boltz2,Boltz Gen, 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

Preferred

• 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

• 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

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

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…