Senior Scientist, Computational Protein Design

Flagship Pioneering • Boston, MA

1d • $146,000 - $209,000

About The Position

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. 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. generative design , automated synthesis , and rapid experimental screening to enable iterative optimization at scale. 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 , miniproteins , and binders engineering and are eager to push the boundaries of non-natural protein design in a fast-moving, data-rich environment.

Requirements

• 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, Boltz2, BoltzGen, 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

Nice To Haves

• 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

Responsibilities

• 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

Benefits

• 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
• healthcare coverage
• annual incentive program
• retirement benefits
• a broad range of other benefits

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: Ph.D. or professional degree