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← Ginkgo Bioworks Inc.

Cheminformatics & Synthesis Prediction

Ginkgo Bioworks Inc.
Location
Boston, Massachusetts
Posted
26 days ago
Department
Datapoints Small Molecule Developability
What they actually want (must-haves)
  • Ph.D. in cheminformatics, computational chemistry, organic chemistry, medicinal chemistry, or a closely related quantitative field, plus 3 years of relevant industry or postdoctoral experience; or an M.S. with 6 years, or a B.S. with 9 years, of relevant experience
  • Strong practical experience in cheminformatics and reaction prediction, including experience with retrosynthesis, reaction-condition prediction, synthetic accessibility, or related workflows
  • Experience working with reaction SMARTS, functional-group classification, molecular representations, and chemical structure data
  • Production experience with RDKit or an equivalent cheminformatics toolkit
  • Experience working with large chemical or vendor building-block catalogs and understanding the trade-offs involved in coverage, scale, and data quality
  • Strong Python skills and experience writing code that others can run and maintain
Nice to have
  • Experience with large makeable or synthesizable chemical spaces, whether commercial or in-house
  • Experience operating a combinatorial library-enumeration pipeline or reaction-prediction workflow in production
  • Experience evaluating predictive models, including uncertainty estimation, calibration, applicability domain, or ranked candidate generation
  • Experience with regiochemistry, stereochemistry, chemical registration systems, ELN/LIMS integration, or chemical data standards
  • Experience connecting computational design to wet-lab results in a design–make–test–learn environment
What the job really is

The Senior Engineer I, Cheminformatics & Synthesis Prediction role at Ginkgo involves developing and maintaining cheminformatics workflows that support the creation of makeable chemical spaces and reaction prediction capabilities. This hands-on position requires collaboration with chemists to translate scientific inquiries into computational workflows, focusing on reaction enumeration and predictive modeling tasks. The role emphasizes practical cheminformatics engineering rather than machine learning research, and it involves writing maintainable code and integrating cheminformatics tools into automated workflows.

Benefits
  • Competitive compensation
  • Generous equity in a public company
  • Robust benefits package including medical, dental & vision coverage
  • Health spending accounts
  • Voluntary benefits
  • Leave of absence policies
Things to weigh
  • No salary listed in the posting, but a range is provided: $115,000 - $165,000
  • Return to office policy requires in-office presence 5 days a week starting October 1, 2025 for employees living within 50 miles of the office
  • The role emphasizes practical cheminformatics engineering over machine learning research, which may limit exposure to cutting-edge ML techniques
Job score3.6/5
Benefits5/5
Freshness4/5
Career value4/5
Role clarity5/5
Pay transparency0/5

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