Senior Scientist, Computational Protein Design

Flagship Pioneering, Inc.•Boston, MA

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. 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. 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 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