Scientific Software Engineer - Computational Chemistry

Aqemia 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 partnerships. Our internal pipeline is growing fast, with several programs in in vivo optimization.

We’re a team of 65+ based in Paris and London, bringing together chemists, physicists, engineers, and machine learning experts to push the boundaries of what’s possible in early-stage drug discovery.

As 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 pipelines.
• Translate scientific strategies into software components that operate at scale.
• Collaborate with ML engineers and platform teams to integrate chemical logic into orchestrated flows.
• Work with internal chemical libraries, molecular formats, and property calculations.
• Ensure robustness, performance, cost effectiveness, and traceability of cheminformatics tools.
• Stay up to date with advances in cheminformatics and contribute to continuous improvement.

What we’re looking for:

• 2 - 4 years of experience in cheminformatics or computational chemistry, ideally in a drug discovery context.
• Strong Python skills and experience with RDKit or similar libraries.
• Familiarity with compound library design, molecular descriptors, and property prediction.
• Ability to work with data scientists, ML engineers, and software teams.
• Strong sense of code quality, testing, and documentation.
• Good communication skills and collaborative mindset.
• Experience in scaling complex scientific logic and reducing computational workload when industrializing research-grade code.

Preferred mindset:

• You’re excited to bring chemistry into the heart of automated scientific workflows.
• You enjoy transforming abstract scientific logic into robust, maintainable, production-grade software.
• You thrive in interdisciplinary environments.
• You’re driven to build tools that make a tangible impact on drug discovery.
• You care about scalability, not just in infrastructure, but also in complexity, efficiency, and scientific throughput.

Why Join Us:

• At 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 models.
• Real-World Impact: Every feature shipped helps scientists prioritise molecules and design better candidates, faster.
• Modern Stack & Challenges: Python, FastAPI, Airflow, Snowflake, Kubernetes, ML workflows, scientific infra, data engineering at scale.
• High Ownership, High Impact: Engineers contribute to architecture, tooling, and scientific decision-making.
• Interdisciplinary Team: Collaborate with chemists, physicists, ML researchers, and product teams.
• Prime Locations: Central Paris or London offices, with 2 remote days/week.
• Strategic Traction: Backed by $100M in funding and a $140M partnership with Sanofi.

Join 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.