Senior Scientist, Computational Protein Design

Flagship Pioneering
Boston, MA USA / Abiologics, Inc2026-02-25

About the job

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.

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

Minimum

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 <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