--- title: 'Cheminformatics & Synthesis Prediction at Ginkgo Bioworks Inc.' canonical: 'https://feeny.ai/job/cheminformatics-synthesis-prediction-ginkgo-bioworks-inc-boston-8fbkktyfwggy' type: 'job' last_seen: '2026-09-12' --- # Cheminformatics & Synthesis Prediction at Ginkgo Bioworks Inc. - **Company:** Ginkgo Bioworks Inc. - **Location:** Boston, MA - **Posted:** 2026-08-25 - **Last confirmed live:** 2026-09-12 - **Apply:** https://job-boards.greenhouse.io/ginkgobioworks/jobs/5220505007 ## Job description Our mission is to make biology easier to engineer. Ginkgo is constructing, editing, and redesigning the living world in order to answer the globe’s growing challenges in health, energy, food, materials, and more. Our bioengineers make use of an in-house automated foundry for designing and building new organisms. 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. By leveraging Ginkgo’s automation and digital infrastructure, Datapoints builds high-quality, large-scale datasets and technical capabilities that accelerate drug discovery and development. The Small Molecules team is looking for a cheminformatics scientist to support the computational work of building and navigating makeable chemical spaces. This includes building the space itself, developing tools that help scientists search and use it, and predicting the outcomes of chemical reactions that connect design to synthesis. ## Role Overview We are hiring a Senior Engineer I, Cheminformatics to develop and operate the cheminformatics workflows behind Ginkgo’s makeable chemical space and reaction-prediction capabilities. This is a hands-on production role spanning two connected areas: building and maintaining large makeable chemical spaces through reaction enumeration, and integrating, evaluating, and improving reaction-prediction workflows such as retrosynthesis and reaction-condition prediction. You will work with reaction templates, molecular representations, functional-group logic, vendor building blocks, predictive models, and reaction data that feeds the design–make–test loop. The ideal candidate combines practical cheminformatics engineering, experience with reaction prediction, and strong chemistry fluency. 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. This is not an ML research position. We prefer to adopt or adapt published methods and open-source tools before building new systems. ## Key Responsibilities Makeable chemical space - Develop and improve reaction-enumeration workflows, including reaction SMARTS templates, functional-group gating, building-block curation, and production runs. - Work with large vendor catalogs while balancing chemical coverage, price, availability, lead time, and data quality. - Improve treatment of regioisomers, stereochemistry, resolution limits, and other sources of ambiguity in enumerated chemical space. - Build reliable workflows for structure handling, reaction execution, sanitization, identifiers, SDF files, and metadata. Reaction prediction and design–make–test workflows - Integrate and evaluate approaches for retrosynthesis, synthetic success, reaction-condition prediction, and related reaction modeling tasks. - Assess models and workflows for calibration, coverage, applicability domain, and practical usefulness; surface uncertainty and risk flags rather than bare point estimates. - Help connect predicted reactions and enumerated compounds to experimental design, make–test workflows, and downstream learning. - Consolidate reaction data—including conditions, yields, failed reactions, and provenance—into a shared, machine-readable source that supports future model improvement. Production platform and collaboration - Write maintainable code and contribute to service-oriented systems, deployment workflows, and data pipelines. - Partner with internal chemists and cross-functional teams to translate scientific questions into reliable computational workflows and interpret results. - Scope and review external or consultant work with clear specifications and acceptance criteria. - Work on commercial digital products by integrating pricing and ordering data and functionalities, and deploying and maintaining related services and tools. - Design, build, and optimize Model Context Protocols (MCPs) and agentic frameworks to support LLM-based work and integrate cheminformatics tools into automated workflows. ## Minimum Qualifications - 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. - Familiarity with service-oriented software, Docker, environment-based configuration, and data pipelines. - Working knowledge of common medicinal-chemistry synthetic transformations and the ability to collaborate effectively with synthetic chemists. - Clear technical communication skills and a disciplined approach to documentation, provenance, and reproducibility. Working Style - You understand that models are mathematical representations of the current state of knowledge: they will never be perfect, but they can support learning and better decisions. You know how to distinguish useful signal from an output that is not reliable enough to use, and communicate uncertainty and limitations clearly. - You balance scientific rigor with practical progress. You make thoughtful trade-offs, avoid overclaiming, and collaborate clearly with chemists and engineers to turn imperfect computational tools into useful workflows. - 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. ## Preferred Qualifications - 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. - Contributions to open-source cheminformatics or experience evaluating third-party chemistry platforms. - Experience building and optimizing Model Context Protocols (MCPs), agentic frameworks, or integrating cheminformatics tools with LLM-based workflows. Why Join Ginkgo Datapoints? - Build cheminformatics technology and workflows on Nebula, the world’s largest autonomous laboratory. - Help connect molecular design, reaction prediction, synthesis, testing, and learning across Ginkgo’s automated platforms. - Develop workflows to ingest, structure, and learn from the high-quality data generated by autonomous laboratory systems. - Join a technically ambitious, cross-functional team building the computational foundations for AI-enabled drug discovery. - Receive competitive compensation, generous equity in a public company, and a robust benefits package. The base salary range for this role is $115,00-165,000. Actual pay within this range will depend on a candidate's skills, expertise, and experience. We also offer company stock awards, a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy. Ginkgo has implemented a return to office policy effective October 1, 2025 with required in office days 5x per week. This policy applies to all employees who live within 50 miles of Ginkgo’s offices in Boston, MA, Emeryville, CA and West Sacramento, CA. It is the policy of Ginkgo Bioworks to provide equal employment opportunities to all employees, employment applicants, and EOE disability/vet. Privacy Notice I understand that I am applying for employment with Ginkgo Bioworks and am being asked to provide information in connection with my application. I further understand that Ginkgo gathers this information through a third-party service provider and that Ginkgo may also use other service providers to assist in the application process.  Ginkgo may share my information with such third-party service providers in connection with my application and for the start of employment.  Ginkgo will treat my information in accordance with Ginkgo's [Privacy Policy](https://www.ginkgobioworks.com/concentric-privacy-policy/).  By submitting this job application, I am acknowledging that I have reviewed and agree to Ginkgo's [Privacy Policy](https://www.ginkgobioworks.com/concentric-privacy-policy/) as well as the privacy policies of the third-party service providers used by Ginkgo's associated with the application process. ## About Ginkgo Bioworks Inc. ## Company Overview - **One-liner**: Ginkgo Bioworks builds and operates autonomous labs that replace manual benchwork with robotics, enabling scientists to program biology for applications across biopharma, agriculture, and industrial biotechnology. - **Entity Type**: Public (NYSE: DNA) - **Headquarters**: Boston, Massachusetts, United States - **Founded**: 2009 - **Founders**: Jason Kelly, Reshma Shetty, Barry Canton, Austin Che, Tom Knight ## Core Business - Primary industry: Biotechnology Research, Synthetic Biology, Autonomous Labs - Target customers: Biopharma, agriculture, and industrial biotech companies (B2B, Enterprise) - Mission: "Build the tools that make biology easier to engineer for everyone" — with a vision that "our children will program biology like we once programmed computers." ## Products & Services - **[Autonomous Lab Platform]**: A robotics-driven laboratory system where scientists can order experimental work to be run by robots, replacing manual benchwork. Available as Ginkgo’s in-house lab or as a "cloud lab" service. - **[Ginkgo Datapoints]**: A contract research service offering small molecule developability, high-throughput screening, and ADME (absorption, distribution, metabolism, excretion) services. - **[Ginkgo Solutions]**: Custom contract research and development services for customer-specific biotech projects. - **[Catalyst Agent]**: A tool that lets scientists "run your experiments on Ginkgo's autonomous lab in Boston, virtually." - **[Biosecurity Software]**: A software offering focused on biosecurity applications. ## Market Standing - **Valuation/Market Cap**: Publicly traded (NYSE: DNA); market cap fluctuates — as of mid-2025, the company had a market cap in the range of ~$1-2 billion (check current quote). IPO date: September 17, 2021. - **Total Funding**: $3.31 billion (cumulative, including IPO and post-IPO equity) - **Key Metric**: Annual Revenue — Not publicly available in search results; the company reports financials in SEC filings. Headcount: ~454 employees (-36% YoY, reflecting a significant restructuring). - **Notable Investors/Partners**: Flagship Pioneering, Takeda, Sanofi, Novartis, Bayer, and others. Key acquisitions include FGen (2022), Circularis Biotechnologies (2022), Altar (2022), Bitome (2022), and AgBiome’s GENESIS Platform (2024). - **Growth Signals**: Trusted by over 130 customers; operates in 10 countries; strong government partnerships (CEO Jason Kelly previously chaired the U.S. National Security Commission on Emerging Biotechnology); active job postings up 175% YoY (though from a low base). ## Competitive Advantages - **Autonomous Lab Leadership**: Ginkgo is pioneering the shift from manual benchwork to fully automated, robot-run labs — a significant moat in productivity and scalability. - **Founding Team**: Founders are pioneers in synthetic biology (e.g., Tom Knight is considered the "father of synthetic biology"; Jason Kelly chaired the U.S. National Security Commission on Emerging Biotechnology). - **Platform Approach**: The "cell programming platform" allows biology to be engineered more like software, enabling applications across diverse markets (food, fragrance, pharmaceuticals). - **Government & Biosecurity Ties**: Deep relationships with U.S. government agencies for biosecurity and national security applications. ## Strategic Focus - **Autonomous Lab Expansion**: Scaling the autonomous lab platform and making it available as a "cloud lab" to external customers. - **Commercialization**: Moving from R&D to commercial revenue through Datapoints and Solutions services. - **Cost Optimization**: The 36% headcount reduction suggests a focus on operational efficiency and path to profitability. - **Biosecurity**: Leveraging government partnerships for biosecurity software and services. ## Why Work Here - **Cutting-Edge Mission**: Work at the intersection of biology, robotics, and software — "program biology like we once programmed computers." - **Engineering Culture**: Heavy emphasis on software engineering for autonomous lab systems (robotics, scheduling, optimization, driver development) — roles for senior software engineers, automation engineers, and hardware engineers. - **Locations**: Primary hub in Boston, Massachusetts (headquarters); second office in Emeryville, California. Some remote roles (e.g., Director, Government Partnership Development). - **Culture**: Described as a place where scientists "focus on insight, creativity, and judgment rather than manual lab work." Internships available in software, automation, and commercial operations. - **Perks**: Not explicitly detailed in search results, but typical for a public biotech: equity, health benefits, and the chance to work on world-changing problems. - **Important Note**: The company has undergone a 36% headcount reduction in the past year — potential job seekers should be aware of restructuring and recent departures of senior leaders (e.g., Head of Commercial, Director of National Security partnerships). ## Sources 1. [ginkgo.bio](https://www.ginkgo.bio/) 2. [ginkgo.bio/about](https://ginkgo.bio/about) 3. [LinkedIn - Ginkgo Bioworks](https://www.linkedin.com/company/ginkgo-bioworks) 4. 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