AI-Driven Drug Discovery Software Engineer (Remote)

Aqemia; Paris; Hybrid; EUR 90,000 - 130,000; Full time

Job summary

AQEMIA is expanding its Engineering team in Paris and London. As a Senior Scientific Software Engineer, you will turn physics-based methods and ML models into scalable software powering our drug discovery platform.

You’ll work with physicists and ML researchers to production‑ise prototypes, shape architecture, and enforce robust engineering standards. This role offers on-site presence in Paris or London with three days on site and two days optional remote, and visa sponsorship options for

Qualifications

• MSc or PhD in computer science, applied mathematics or a related quantitative field, with a background in computational chemistry, molecular simulation or statistical physics.
• 5+ years of software engineering experience, with strong expertise in a cheminformatics context.
• Strong Python skills and experience with RDKit or similar libraries.
• Solid software architecture skills: designing modular, maintainable systems used by several teams.
• Hands‑on experience with CI/CD, containerization (Docker) and workflow orchestration (e.g. Airflow, Prefect, Kubernetes).
• Experience running compute‑intensive workloads at scale on the cloud, including GPUs.
• Ability to work closely with researchers (understanding their methods, challenging prototypes and explaining engineering trade‑offs), with good communication skills and a collaborative mindset.

Responsibilities

• Translate scientific strategies from our StatMech research teams into software components that run at scale.
• Optimize compute‑intensive code (profiling, parallelization, GPU acceleration) and run it reliably at scale on our cloud infrastructure.
• Expose physics‑based calculations through clean APIs that integrate into our technology platform.
• Package ML models fine‑tuned by our AI research teams (generative chemistry, property prediction, etc.) into versioned, reproducible, deployable components, and build scalable, GPU‑efficient inference pipelines.
• Implement MLOps practices, including model and data versioning, experiment tracking, model registry and monitoring.
• Orchestrate ML models and physics‑based calculations into end‑to‑end workflows.
• Co‑lead the architecture of our scientific computing stack and our Python engineering standards: packaging, typing, testing, code review and documentation.
• Contribute to setting up and maintaining CI/CD pipelines and workflow orchestration (e.g. GitHub Actions, Docker, Airflow/Prefect, Kubernetes, Flyte), and stay up to date with advances in cheminformatics.

Skills

Python

RDKit

CI/CD

Docker

Kubernetes

Cloud

Education

MSc or PhD in computer science / math / related quantitative field

Tools

Airflow

Prefect

GitHub Actions

Job description

AQEMIA is expanding its Engineering team in Paris and London. As a Senior Scientific Software Engineer, you will turn physics-based methods and ML models into scalable software powering our drug discovery platform.

You’ll work with physicists and ML researchers to production‑ise prototypes, shape architecture, and enforce robust engineering standards. This role offers on-site presence in Paris or London with three days on site and two days optional remote, and visa sponsorship options for