Abiologics, Inc | Boston, MA Senior Scientist, Computational Protein Design
Flagship Pioneering, Boston, MA, United States
Senior Scientist, Computational Protein Design
Boston, MA USA
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. Synteins™ 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 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.
Key Responsibilities
Design and execute Synteins™ engineering campaigns to generate drug candidates.
Create computational design strategies to deliver drug candidates drawing from an 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.
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, 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.
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.
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.
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.
The salary range for this role is $146,000 - $209,000.
Abiologics, Inc currently offers healthcare coverage, an annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc's good faith estimate as of the date of publication and may be modified in the future.
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Boston, MA USA
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. Synteins™ 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 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.
Key Responsibilities
Design and execute Synteins™ engineering campaigns to generate drug candidates.
Create computational design strategies to deliver drug candidates drawing from an 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.
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, 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.
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.
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.
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.
The salary range for this role is $146,000 - $209,000.
Abiologics, Inc currently offers healthcare coverage, an annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Abiologics, Inc's good faith estimate as of the date of publication and may be modified in the future.
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