Hybrid Computational Protein Design Scientist I

Generate Biomedicines; Somerville (MA); Hybrid; USD 140,000 - 210,000; Full time

Job summary

Generate Biomedicines seeks a creative Computational Protein Design Scientist to join our Model-Driven Design team in Somerville, MA. You will work at the intersection of machine learning, structural biology, and therapeutic development, driving de novo protein design and benchmarking in rapid design–build–test–learn cycles to advance our pipeline.

The ideal candidate has a PhD and hands-on ML experience for protein design, with a strong coding background in Python and a track record of

Qualifications

• PhD in Computational Biology, Biophysics, Computer Science, or related field with protein design experience.
• 0–2 years of experience applying computational/ML methods to protein design.
• Hands-on experience with ML and generative modeling for protein design (e.g., RFDiffusion, ProteinMPNN).
• Strong structural intuition and understanding of protein biophysics.
• Familiarity with protein therapeutic modalities (antibodies, mini-proteins, VHHs, peptides, enzymes).
• Proficiency in Python and scientific computing; production-grade code experience.

Responsibilities

• Develop, validate, and productionize de novo protein generation protocols and optimization techniques.
• Define and implement in silico metrics for evaluating designs and benchmarking.
• Benchmark foundation models and guide their application across therapeutic targets.
• Propose new therapeutic strategies using de novo tools and modalities.
• Collaborate cross-functionally with experimental teams to guide iterative design-build-test-learn cycles.
• Advance state-of-the-art sequence–structure–function understanding with reusable platforms.
• Integrate agentic AI tools to accelerate discovery and develop production-quality tools.

Skills

Python programming

ML for protein design

Structural biology intuition

Experimental bench understanding

Education

PhD in Computational Biology, Biophysics, Computer Science, or related field

Tools

RFDiffusion

ProteinMPNN

BindCraft

BoltzDesign

Job description

Generate Biomedicines seeks a creative Computational Protein Design Scientist to join our Model-Driven Design team in Somerville, MA. You will work at the intersection of machine learning, structural biology, and therapeutic development, driving de novo protein design and benchmarking in rapid design–build–test–learn cycles to advance our pipeline.

The ideal candidate has a PhD and hands-on ML experience for protein design, with a strong coding background in Python and a track record of