Scientific Software Engineer - Computational Chemistry

About AQEMIA

AQEMIA is a drug invention company dedicated to creating entirely new medicines to address major unmet medical needs.

At the core of our mission is QEMI , our proprietary molecule‑invention platform, which uniquely combines cutting‑edge science with advanced technology. Powered by physics‑based modeling, statistical mechanics, and generative AI, QEMI allows our teams to design novel drug candidates from first principles.

What makes AQEMIA different is our commitment to true innovation: our research is dedicated to the invention of new molecular entities, not the refinement of existing ones. We focus on inventing never‑before‑seen molecules , without relying on experimental data, and advancing them into a growing pipeline of proprietary programs and strategic partnerships with leading pharmaceutical companies.

Our most advanced preclinical programs are currently in in vivo optimization , targeting diseases still waiting for effective treatments, offering our teams the opportunity to work on science that can make a real difference in people’s lives.

For more information, visit AQEMIA.com and our LinkedIn.

About our Team

AQEMIA brings together a diverse, multidisciplinary team of 65+ professionals based in Paris and London. Our scientists and engineers, including chemists, physicists, machine learning experts, and software engineers, work side by side to push the boundaries of early‑stage drug discovery.

This close collaboration across disciplines is central to our approach, enabling us to tackle complex scientific challenges from first principles and translate cutting‑edge ideas into novel therapeutic candidates. At AQEMIA, team members are encouraged to contribute their expertise, learn from one another, and play an active role in shaping the future of drug invention.

The Role

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, we are driven by a bold mission: transforming the way drugs are discovered. Here, 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 prioritize 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.