Cheminformatics & Synthesis Prediction
Ginkgo Bioworks Inc.11 days ago
Boston, MA, USASenior
Base Salary
$115k - $165k/yr
Responsibilities
- Develop and improve reaction-enumeration workflows using reaction SMARTS templates, functional-group gating, building-block curation, and production runs.
- Manage large vendor catalogs while balancing chemical coverage, price, availability, lead time, and data quality.
- Improve handling of regioisomers, stereochemistry, resolution limits, structure execution, sanitization, identifiers, SDF files, and metadata.
- Integrate and evaluate retrosynthesis, synthetic-success, reaction-condition prediction, and related reaction-modeling workflows.
- Assess model calibration, coverage, applicability domain, practical usefulness, uncertainty, and risk flags.
- Connect predicted reactions and enumerated compounds to experimental design, make–test workflows, and downstream learning.
- Consolidate reaction conditions, yields, failed reactions, and provenance into a shared machine-readable data source.
- Write maintainable code and contribute to service-oriented systems, deployment workflows, data pipelines, digital products, and related services.
- Collaborate with chemists and cross-functional teams, scope external work, and translate scientific questions into reliable computational workflows.
- Design and optimize Model Context Protocols and agentic frameworks integrating cheminformatics tools into automated LLM-based workflows.
Requirements
- A Ph.D. in cheminformatics, computational chemistry, organic chemistry, medicinal chemistry, or a related quantitative field plus 3 years of relevant experience; or an M.S. plus 6 years; or a B.S. plus 9 years.
- Strong practical experience in cheminformatics and reaction prediction, including retrosynthesis, reaction-condition prediction, synthetic accessibility, or related workflows.
- Experience with reaction SMARTS, functional-group classification, molecular representations, and chemical structure data.
- Production experience with RDKit or an equivalent cheminformatics toolkit.
- Experience with large chemical or vendor building-block catalogs and their coverage, scale, and data-quality trade-offs.
- Strong Python skills and experience writing maintainable code.
- Familiarity with service-oriented software, Docker, environment-based configuration, and data pipelines.
- Working knowledge of common medicinal-chemistry synthetic transformations and ability to collaborate with synthetic chemists.
- Clear technical communication and disciplined documentation, provenance, and reproducibility practices.
- Preferred qualifications include production operation of chemical-space or reaction-prediction workflows, predictive-model evaluation, chemical registration systems, ELN/LIMS integration, chemical data standards, design–make–test–learn environments, open-source cheminformatics, chemistry platforms, MCPs, agentic frameworks, or LLM-based workflows.
Benefits
- Competitive compensation, company stock awards, medical, dental, and vision coverage, health spending accounts, voluntary benefits, leave policies, a 401(k) with employer contribution, paid holidays, a full-week winter shutdown, and unlimited paid time off.
- The role follows a return-to-office policy requiring five days per week in the office for employees living within 50 miles of specified Ginkgo offices in Boston, Emeryville, or West Sacramento.