Senior Scientist, Computational Protein Design at Flagship Pioneering, Inc.

Boston, Massachusetts, United States -

Full Time

Start Date

Immediate

Expiry Date

27 May, 26

Salary

209000.0

Posted On

26 Feb, 26

Experience

2 year(s) or above

Remote Job

Yes

Telecommute

Yes

Sponsor Visa

Skills

Protein Design, Computational Design, Structural Biology, Protein Engineering, De Novo Protein Design, Miniproteins, Binders Engineering, AI-enabled Platform, Generative Design, Rosetta Scripts, ML Tools, Solubility Optimization, Stability Optimization, RFdiffusion, ProteinMPNN, AF2

Industry

Biotechnology Research

Description

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 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 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., 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 Excellent communication skills Preferred Experience designing minibinders or proteins

Responsibilities

The role involves designing and executing Synteins engineering campaigns to generate drug candidates, utilizing computational design strategies that incorporate Machine Learning tools and Rosetta scripts. Responsibilities also include collaborating across disciplines to optimize designs for function, solubility, and stability, integrating structural and biophysical data into iterative optimization cycles.