Scientific Software Engineer - Computational Chemistry

About AqemiaAqemia is a next-generation pharmatech reinventing drug discovery with quantum-inspired physics and generative AI.Our mission: design innovative small-molecule drug candidates for dozens of critical diseases, faster and smarter, without relying on experimental data.Unlike traditional approaches, Aqemia starts drug discovery purely in silico. By combining physics-based models with large language models trained on proprietary data, we identify promising molecules with high accuracy before synthesis.We\’ve already delivered multiple preclinical successes and secured strategic partnership. Our internal pipeline is growing fast, with several programs in in vivo optimization.We\’re a team of 65+ based in Paris and London, we bring together chemists, physicists, engineers, and machine learning experts to push the boundaries of what\’s possible in early-stage drug discovery.The RoleAs a Scientific Software Engineer in the product team supporting the daily activities of scientists (physics, ML, deep learning) producing predictors and prediction workflows,you\’ll contribute to scaling the scientific logic and software that connect Aqemia\’s predictive models into advanced drug discovery workflows.You\’ll build the engine that enables large-scale computation and seamless data transformation.You\’ll work at the interface of cheminformatics, software engineering, and platform infrastructure, translating scientific needs into robust, scalable tools used daily across Aqemia\’s pipeline.What you\’ll do Build, scale, and maintain cheminformatics predictors and workflows that power multi-step prediction pipelinesTranslate scientific strategies into software components that operate at scaleCollaborate with ML engineers and platform teams to integrate chemical logic into orchestrated flowsWork with internal chemical libraries, molecular formats, and property calculationsBuild, scale, and maintain cheminformatics predictors and workflows that power multi-step prediction pipelinesEnsure robustness, performance, cost effectiveness, and traceability of cheminformatics toolsStay up to date with advances in cheminformatics and contribute to continuous improvementWhat we\’re looking for 2 – 4 years of experience in cheminformatics or computational chemistry, ideally in a drug discovery contextStrong Python skills and experience with RDKit or similar librariesFamiliarity with compound library design, molecular descriptors, and property predictionAbility to work with data scientists, ML engineers, and software teamsStrong sense of code quality, testing, and documentationGood communication skills and collaborative mindsetExperience in scaling complex scientific logic and reducing computational workload when industrializing research-grade codePreferred mindset You\’re excited to bring chemistry into the heart of automated scientific workflowsYou enjoy transforming abstract scientific logic into robust, maintainable, production-grade softwareYou thrive in interdisciplinary environmentsYou\’re driven to build tools that make a tangible impact on drug discoveryYou care about scalability, not just in infrastructure, but also in complexity, efficiency, and scientific throughputWhy Join UsAt Aqemia, engineers don\’t just build software, they help discover real drugs.You \’ll work at the intersection of AI, physics and chemistry, transforming bold scientific ideas into robust, production-grade tools that accelerate discovery.DeepTech Mission : Build the platform that powers AI-driven drug discovery, combining quantum-inspired physics with generative modelsReal-World Impact : Every feature shipped helps scientists prioritize molecules and design better candidates, fasterModern Stack & Challenges : Python, FastAPI, Airflow, Snowflake, Kubernetes, ML workflows, scientific infra, data engineering at scaleHigh Ownership, High Impact : Engineers contribute to architecture, tooling, and scientific decision-makingInterdisciplinary Team : Collaborate with chemists, physicists, ML researchers, and product teamsPrime Locations : Central Paris or London offices, with 2 remote days/weekStrategic Traction : Backed by $100M in funding and a $140M partnership with SanofiJoin us if you\’re excited to shape the future of AI-driven drug discovery, and want your code to change the course of real diseases.

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