Senior Director, Computational Drug Discovery

About Apheris

At Apheris, we are building the future of how AI is applied in pharmaceutical R&D. 
Our federated computing technology enables global pharma companies to collaborate securely on large AI models that accelerate drug discovery, without ever sharing their proprietary data. By powering multi-partner data networks across small molecules, antibodies, and protein folding, Apheris is redefining how science and AI intersect.

Apheris is a neutral technology and solutions provider. We do not conduct internal drug discovery research, and we do not develop proprietary drug assets. Instead, we support pharmaceutical computational drug discovery teams with production-grade applications, models, and infrastructure that help advance their own drug programs.

We currently host two flagship networks: the AI Structural Biology (AISB) Network, focused on protein co-folding and binding affinity prediction, and the ADMET Network, focused on small-molecule property prediction. In addition, we have just launched ApherisFold, an enterprise co-folding solution that enables pharma teams to deploy cutting-edge models such as OpenFold 3 and Boltz-2 directly within their own environments.

About the role

We are looking for a Senior Director, Computational Drug Discovery to build and lead a small, high-impact computational drug discovery team and to serve as a peer-level scientific counterpart to senior computational chemistry and drug discovery leaders at the world’s leading pharmaceutical companies.

You will work closely with Product, ML/AI, and Commercial teams to shape how Apheris’ applications, models, and data networks are applied to drug programs of our customers. Your role is to ensure that scientific direction, workflows, and recommendations are grounded in how drug discovery is actually executed in industry and deliver measurable value in practice.

This is a hands-on, externally facing leadership role. It requires strong industry credibility, comfort giving and challenging scientific direction, and the ability to engage directly with senior scientific stakeholders at our pharma customers. You will lead a team of application scientists with a background in computational or medicinal chemistry. You maintain a strong working understanding of modern ML approaches in drug discovery and their practical implications and are comfortable operating hands-on in a fast-paced, venture-backed, remote-first environment.

What you will do

• Own scientific direction across modalities, data, and workflows
  • Define which drug discovery problems, modalities, and data types Apheris prioritizes with our product offerings.
  • Guide how applications and models should evolve to remain maximally useful to pharma teams.
  • Balance scientific ambition with practicality and adoption in customer environments.
  • Own the “why” and high-level structure of new scientific initiatives and proposals, while partnering closely with internal ML and science teams on detailed methodology and execution.
• Build and lead an established, growing computational drug discovery team
  • Lead a core team already in place, including a senior medicinal chemist and a forward-deployed scientist, both with top-tier academic and industry backgrounds.
  • Hire and integrate 1–2 additional team members over the next 6–9 months as customer demand scales.
  • Set clear direction and execution standards across all customer-facing programs.
  • Oversee scientific quality and program enablement rather than personally owning detailed technical implementation.
• Act as the senior counterpart to pharma R&D leaders
  • Engage comfortably and credibly with leading computational drug discovery scientists at large pharmaceutical companies.
  • Lead deep scientific discussions on program strategy, model application, and decision-making trade-offs.
  • Provide authoritative guidance grounded in real-world drug discovery experience.
  • Serve as the visible scientific face to customers, including at senior leadership level.
    
• Represent Apheris in the ecosystem
  • Build trust and credibility through talks and direct engagement with the community.
  • Strengthen Apheris’ reputation as a serious, neutral partner for computational drug discovery.
  • Contribute to strategic narratives around why federated and AI-driven approaches enable better drug programs, supported by internal ML and science teams for technical manuscript writing.
  • Oversee and challenge program-level recommendations to ensure strategic alignment and scientific rigor.
• Drive hands-on scientific leadership across customer programs
  • Give concrete, actionable scientific direction to application scientists and customer teams.
  • Ensure recommendations reflect how discovery programs are actually run, not theoretical workflows.
  • Review and challenge analyses, models, and conclusions to maintain a high scientific bar.
• Partner closely with Product and ML/AI teams
  • Translate customer needs and scientific insight into clear product and model requirements.
  • Shape prioritization decisions by grounding them in customer impact and discovery realities.
  • Act as a scientific bridge between customers and internal development teams.

What we expect from you

• PhD in computational chemistry, cheminformatics, computational drug discovery, or a closely related field.
• 8+ years of post-PhD industry experience in computational drug discovery or computational chemistry, including proven impact on drug discovery programs from hit finding through lead optimization.
• Strong practical understanding of structure-based and ligand-based design, ADMET modelling, and integration of experimental and biophysical data in real drug programs.
• Solid understanding of modern ML approaches in drug discovery, with sound judgment on where ML materially improves outcomes.
• Strong scientific credibility, demonstrated through prior roles at leading pharma, top-tier biotech, or recognized computational drug discovery technology providers, and ideally a solid publication record.
• Demonstrated experience leading and mentoring computational drug discovery teams.
• Comfortable operating hands-on in a fast-moving, venture-backed, remote-first environment.
• Clear motivation to enable customer drug discovery programs rather than run internal pipelines.

Nice to have

• Background as an application scientist at a leading computational chemistry or drug discovery software provider.
• Experience leading computational drug discovery teams at a TechBio or advanced biotech.
• Prior exposure to federated, multi-partner data collaborations.
• Experience shaping product direction for scientific software platforms.

What we offer you

• Direct collaboration with world-leading computational drug discovery scientists across major pharmaceutical companies.
• A leadership role with real influence on company direction, scientific priorities, and product strategy, working closely with the founders.
• Regular interaction with our Scientific Advisory Board and external experts at the forefront of the field.
• The opportunity to build and scale the computational drug discovery function from the ground up.
• Competitive compensation, including meaningful early-stage virtual share options.
• Generous holiday allowance
• Great suite of benefits, including a wellbeing budget, mental health benefits, a work-from-home budget, a co-working stipend and a learning and development budget
• Remote-first working – work where you work best, whether from home or a co-working space near you
• Office Days at our Berlin HQ or a different European location (3x a year)