Computational Chemist

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 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, our WTTJ Page, and our LinkedIn.

About our Team

AQEMIA brings together a diverse, multidisciplinary team of 80+ 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

AQEMIA is building a new generation of AI-driven drug discovery workflows, and this role is critical to scaling the speed and reliability of our pre-program screening operations. As Computational Chemist – Pre-Programs, you will own the end-to-end execution and monitoring of QEMI virtual screening and hit expansion campaigns, from structure selection and target preparation to active hit selection. This role exists to remove operational bottlenecks that currently depend on build-team capacity, enabling pre-programs to progress with greater autonomy, consistency, and throughput.

You will combine scientific judgment, operational ownership, and hands-on problem solving to ensure screening campaigns are delivered with high quality and reproducibility across all active pre-programs. Beyond execution, you will play a key role in identifying why runs succeed or fail and translating those learnings into actionable feedback for platform and product teams. Within 12 months, success in this role will mean a standardized, resilient, and scalable screening workflow that accelerates AQEMIA’s ability to identify high-quality hits across multiple discovery programs.

Responsibilities

-

Own the end-to-end execution and monitoring of QEMI virtual screening and hit expansion campaigns across all active pre-programs

-

Select and prepare appropriate protein structures based on target biology, binding site context, and program objectives

-

Run and interpret screenability assessments, configure workflows, and coordinate screening execution with compute and engineering teams

-

Apply compound filtering and selection workflows, ensuring compounds meet registration, traceability, and screenability standards

-

Active contributor to pre-programs prioritization strategy by doing retrospectives of the screens, and identifying areas of improvement

-

Troubleshoot underperforming runs and identify structural, methodological, or operational improvements to increase hit quality and workflow reliability

-

Partner with engineering and platform teams to standardize, document, and progressively automate the run process as the platform evolves

-

Maintain robust operational documentation and backup processes to ensure continuity and resilience across team changes and scaling needs

Qualifications

-

Strong background in computational chemistry, cheminformatics, or computer-aided drug design (CADD)

-

Experience with structure-based virtual screening workflows, docking, scoring, and hit triage

-

Ability to independently assess protein structure quality and make scientific decisions on structure selection and screening strategy

-

Strong working knowledge of Python and scientific scripting workflows, including troubleshooting and modifying existing pipelines

-

Comfortable working in Linux environments and with command-line tools, configuration files, and automated workflows

-

Familiarity with chemical data handling and compound registration workflows, including SMILES and RDKit

-

Minimum 6 years of relevant experience in computational chemistry or related scientific fields

Nice‑to‑Have

-

Experience supporting early discovery or preclinical drug discovery programs in biotech or pharma

-

Familiarity with protein folding methods and structure prediction workflows

-

Understanding of medicinal chemistry concepts such as drug-likeness, developability, and ADMET

-

Experience contributing operational insights into platform or product improvement roadmaps

-

Prior experience scaling or standardising scientific workflows across multiple programs

Please note that Aqemia currently only offers visa sponsorship for roles based in our Paris location.

Why Join Us ?

At AQEMIA, we work for a mission: joining us means having your own impact on changing the way drugs are discovered, and helping to shape the direction of our fast-growing company and team.

Expanding Drug Discovery Pipeline : Focused on critical therapeutic areas like Oncology, CNS, Immuno-inflammation... with in vivo proof of concept/patent stage programs. Collaborations with top Pharma, including a $140M Sanofi deal.

World-Class Interdisciplinary Team : work alongside exceptional talent at the intersection of technology and life sciences. Our teams combine deep expertise in AI, physics-based modeling, biology, and medicinal chemistry to push the boundaries of innovation.

DeepTech Recognition: AQEMIA is proud to be part of the French Tech 120 and France 2030, highlighting our role as a key player in Europe’s DeepTech ecosystem.

Prime Location with Flexibility : Our offices are located in the heart of Paris and London (King’s Cross), with flexible work arrangements including up to two remote days per week.

Strong Financial Backing : $100M raised from leading European and International investors