Staff Engineer, Chemical Search

Satomic•San Diego, CA

7d•$180,000 - $200,000

About The Position

This first cheminformatics hire will design and build the chemistry search engine: the system that exposes our accessible chemical space through query modes fit for how our partners actually design molecules and run their discovery campaigns. This engine will be searched by generative models, AI agents, and medicinal chemists alike. The engine is grounded in predictive models that capture the actual capabilities of our platform rather than a static catalog, which changes the underlying architecture in ways an experienced builder in this space will already have opinions about. You will take in constraints from our automation team, conversion and substrate-scope models from our ML team, and building blocks from our vendors to define the complete specification of Satomic's accessible chemical space. You will also translate insights from our partners’ discovery strategies into fit-for-purpose query modes, keeping the engine in sync as both Satomic's accessible chemistry expands and our partners' discovery workflows evolve. This role is a founding-engineer position within the Development team. You'll be the technical owner of the cheminformatics domain — defining its standards and its architecture — while working as part of a broader engineering group that owns the platform you're building on. You will partner closely with our data science / ML lead and work day-to-day with the rest of Development on the systems your engine integrates with. You will have exposure to end users at Satomic’s commercial partners to translate user behavior into the query types the engine should support. We believe being part of the chemistry-AI conversation externally (through publication, open source, and the conferences and forums where this field develops) is part of the job. This is a hands-on role for an engineer who thrives with extreme latitude, ownership, and judgment. You will decide what to build versus buy on cheminformatics-specific tooling (RDKit / OpenEye for chemistry primitives, AiZynthFinder / ASKCOS / Synthia / IBM RXN for retrosynthesis, pharmacophore tooling, IP / FTO filtering, vector index choice), choose the engine's core representations, and define the versioning rules that keep it correct as chemistry capabilities expand.Infrastructure-adjacent choices — vector index, storage layer, serving framework — are made jointly with the team. As Satomic’s first cheminformatics engineer, you will be the technical owner of this domain: you will be the sole individual contributor driving this work directly for the first several months, with the opportunity to build a team under you within year one as the surface area grows.

Requirements

Track record of owning a production chemistry search (or closely analogous retrieval / indexing system over structured scientific data) end-to-end in production, with real users on a customer-facing critical path.
Delivered sub-second p95 for interactive query workloads and sustained high-throughput batch scoring (think 10k+/second).
Knowledge of architectural calls for performance.
Ability to think in hot paths, indexing strategies, and inference at scale.
Ability to make decisions that survive both growth and change in the underlying domain.
Production-level fluency with core cheminformatics tooling (RDKit and/or OpenEye).
Understanding of molecule and reaction representations, with strong opinions about when each is the right primitive.
Working experience with at least one major retrosynthesis system in production.
Ability to articulate what a retrosynthesis layer for a defined-capability platform should do differently, specifically when narrowly scoped against validated reactions.
Direct experience with generative chemistry methods, or the confidence and track record to become an expert on generative chemistry sampling and how accessible-space engines are best exposed to it.
Enough chemistry intuition to hold a technical conversation with a medicinal or synthetic organic chemist as a peer.
Confidence making build-vs-buy decisions across third-party cheminformatics tooling.
Track record of integrating, extending, or deliberately replacing third-party tooling.
Solid engineering fundamentals with room to grow.
Python proficiency required.
Genuine enthusiasm for software engineering.
Curiosity about expanding toolkit.
Excitement to pick up new languages and explore where different tools shine.
Comfort reasoning about how code performs.
Eagerness to keep learning.

Nice To Haves

Familiarity with data stores or vector indexes (FAISS, ScaNN, pgvector, or similar).
Experience with performance-oriented languages like Rust, Go, or C++.

Responsibilities

Design and build the chemistry search engine.
Expose accessible chemical space through query modes.
Ground the engine in predictive models.
Define the complete specification of Satomic's accessible chemical space.
Translate insights from partners’ discovery strategies into fit-for-purpose query modes.
Define standards and architecture for the cheminformatics domain.
Partner closely with the data science / ML lead.
Work day-to-day with the rest of Development on system integrations.
Translate user behavior into query types the engine should support.
Decide what to build versus buy on cheminformatics-specific tooling.
Choose the engine's core representations.
Define versioning rules for the engine.
Make infrastructure-adjacent choices jointly with the team.
Build and prioritize query modes (e.g., bounded enumeration, generative sampling, neighborhood and analog generation, structure search, retrosynthetic accessibility scoring of arbitrary external molecules).
Integrate conversion prediction and substrate-scope models as the accessibility scoring function.
Implement yield- and scale-aware multi-step path search.
Manage versioning, capability-snapshot, and cache-invalidation discipline.
Define the cheminformatics function at Satomic: its standards, hiring bar, and team.
Build the engine into a multi-mode product used by paying customers.
Deliver exact retrosynthesis for external query molecules.
Expose the accessible space cleanly to partner generative chemistry workflows.
Make the accessible space a publishable, defensible asset.
Become a recognized voice in the external chemistry-AI conversation.
Hire and onboard the first cheminformatics engineer(s) under you.
Define the technical screen for hiring.
Build Satomic’s chemistry search engine into the industry reference for synthesis-aware design space.
Establish yourself as one of the field’s authoritative voices on synthesis-aware chemical space.
Establish Satomic’s cheminformatics function as the destination for top talent.
Lead a team that consistently raises the bar.
Steward the engine through multiple generations of chemistry capability expansion.
Become the organizational reference point for how Satomic represents, searches, and reasons about chemistry at scale.