Flagship Pioneering Company
(Senior) Scientist, Protein Design
Flagship Pioneering Company, Boston, Massachusetts, us, 02298
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Company Description 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.
THE ROLE 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
Required PROFESSIONAL EXPERIENCE & QUALIFICATIONS
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
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 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
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.
Location Cambridge, MA
#J-18808-Ljbffr
Company Description 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.
THE ROLE 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
Required PROFESSIONAL EXPERIENCE & QUALIFICATIONS
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
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 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
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.
Location Cambridge, MA
#J-18808-Ljbffr