Ginkgo Bioworks

Ginkgo Bioworks

Cheminformatics & Synthesis Prediction

Boston, Massachusetts · Senior

Sponsorship not specified$12k-$165kDetected 58 days ago
PythonDockerMachine LearningLLMsAccessibilityResearchExperimental DesignCommunicationCollaboration

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odds of building a lasting career here

47Sponsors, lottery-bound
Cap-exempt (no lottery)0
Sponsors this role80
Entry-level history0
PERM / green-card track0
Lottery odds (Level II)66
Fits your clock70

Sponsors, but it's cap-subject — you still face the weighted lottery (~30% per draw at Level II). Good if you win; have a cap-exempt backup on your list.

Lottery odds assume a STEM candidate.

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About the role

  • Internal chemists provide deep synthetic and medicinal chemistry expertise
  • your role is to translate their questions into reliable computational workflows and explain what the systems did and why.
  • Internal chemists provide deep synthetic and medicinal chemistry expertise; your role is to translate their questions into reliable computational workflows and explain what the systems did and why.

Responsibilities

  • Develop and improve reaction-enumeration workflows, including reaction SMARTS templates, functional-group gating, building-block curation, and production runs.
  • Build reliable workflows for structure handling, reaction execution, sanitization, identifiers, SDF files, and metadata.
  • Reaction prediction and design-make-test workflows
  • Consolidate reaction data-including conditions, yields, failed reactions, and provenance-into a shared, machine-readable source that supports future model improvement.
  • Partner with internal chemists and cross-functional teams to translate scientific questions into reliable computational workflows and interpret results.

Requirements

  • 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.
  • Familiarity with service-oriented software, Docker, environment-based configuration, and data pipelines.
  • You know how to distinguish useful signal from an output that is not reliable enough to use, and communicate uncertainty and limitations clearly.
  • You are intellectually curious and impatient with the status quo, with a passion for establishing and advancing state-of-the-art computational methods in practical production settings.

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.
  • Contributions to open-source cheminformatics or experience evaluating third-party chemistry platforms.
  • Why Join Ginkgo Datapoints?
  • Actual pay within this range will depend on a candidate's skills, expertise, and experience.
  • Ginkgo has implemented a return to office policy effective October 1, 2025 with required in office days 5x per week.

Skills

  • Senior Engineer I, Cheminformatics & Synthesis Prediction
  • Boston, Massachusetts
  • About Ginkgo Datapoints
  • Ginkgo Datapoints, a business unit within Ginkgo Bioworks, is ushering in the coming era of AI-backed biotechnology breakthroughs.

Compensation

  • Receive competitive compensation, generous equity in a public company, and a robust benefits package.

Benefits

  • Work with large vendor catalogs while balancing chemical coverage, price, availability, lead time, and data quality.
  • Assess models and workflows for calibration, coverage, applicability domain, and practical usefulness
  • Help connect predicted reactions and enumerated compounds to experimental design, make-test workflows, and downstream learning.

Company info

  • Our mission is to make biology easier to engineer.
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This listing is sourced directly from Ginkgo Bioworks's careers page and normalized into a canonical job model.