Staff Engineer, Chemical Search at Satomic

San Diego, California, United States -

Full Time

Start Date

Immediate

Expiry Date

28 Aug, 26

Salary

200000.0

Posted On

30 May, 26

Experience

10 year(s) or above

Remote Job

Yes

Telecommute

Yes

Sponsor Visa

Skills

Cheminformatics, Python, RDKit, OpenEye, Graph Search, Indexing, Retrosynthesis, Generative Chemistry, Vector Indexes, Software Architecture, API Design, Data Structures, Chemical Search Engines, Inference at Scale, System Design, Performance Optimization

Industry

Chemical Manufacturing

Description

About the role 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. Expected Outcomes By day 30, you will have: Identified the open architectural decisions for v1 (internal representation, query modes, inference layer, build-vs-buy on retrosynthesis tooling, versioning strategy) and written your prioritization rationale clearly enough to be debated and built on. Working command of Satomic’s reaction set, condition profiles, conversion models, substrate clusters, and multi-step path constraints, to the point that you can explain the accessible space to a new hire on a whiteboard. Shipped a tangible internal accessibility tool that lets the team query the current chemistry capability for at least one query mode, used in a real prospect or program decision within the first month. By day 90, you will have: Delivered a v1 chemistry search engine in production at our commercial launch: forward-first, synthon-aware, with at least two customer-facing query modes wired end-to-end against the live platform. Defined and documented the engine’s internal representation, indexing strategy, and serving architecture, including which paths are hot, what is materialized, and how the system maintains low latency under each query mode. Established the integration contract with conversion prediction models as the accessibility scoring function, and with the synthesis-execution layer with our Software team as the downstream consumer. Set the versioning and cache-invalidation discipline that lets the engine function with weekly chemistry capability changes. By Year 1, you will have: Built the engine into a multi-mode product used by paying customers and integrated into their design workflows. Delivered exact retrosynthesis, narrowly scoped against Satomic's validated reaction set, for external query molecules, paired with the learned accessibility model, with a clear story for when each is invoked. Exposed the accessible space cleanly to partner generative chemistry workflows, with an interface fit for de novo molecule scoring, constrained sampling, and batch evaluation at the latencies these pipelines actually need. Made the accessible space a publishable, defensible asset (ie, a credible answer to “how is this different from Enamine REAL” that holds up to medicinal-chemist scrutiny), and become a recognized voice in the external chemistry-AI conversation. Hired and onboarded the first cheminformatics engineer(s) under you, and defined the technical screen that consistently surfaces high-signal candidates in this rare niche. By Year 5, you will have: Built Satomic’s chemistry search engine into the industry reference for synthesis-aware design space. Established yourself as one of the field’s authoritative voices on synthesis-aware chemical space and its interface to generative chemistry Established Satomic’s cheminformatics function as the destination for top talent in this niche, leading a team that consistently raises the bar. Stewarded the engine through multiple generations of chemistry capability expansion without architectural debt that slows the platform’s growth. Become the organizational reference point for how Satomic thinks about representing, searching, and reasoning about chemistry at scale. What You Will Own The chemistry search engine: internal representation, indexing strategy, query-mode logic, and the inference layer. Platform integration is delivered in collaboration with the broader Development team. Building and prioritizing query modes (e.g., bounded enumeration, generative sampling, neighborhood and analog generation, structure search, retrosynthetic accessibility scoring of arbitrary external molecules), shaped by partner discovery workflows. Build-vs-buy decisions on cheminformatics-specific tooling (RDKit/OpenEye, retrosynthesis systems, pharmacophore tooling). Architecture decisions that touch shared infrastructure are made jointly with the team. Integration of the platform's conversion prediction and substrate-scope models as the accessibility scoring function, moving beyond SA/SCScore-style static heuristics to a platform-grounded measure of what Satomic can actually make. Yield- and scale-aware multi-step path search that prefers front-loading low-yield steps. The versioning, capability-snapshot, and cache-invalidation discipline that keeps the engine coherent as the underlying chemistry definition evolves. The cheminformatics function at Satomic: its standards, its hiring bar, and its team as it grows. What This Role Is (and Is Not) This role is: A principal-level role with broad technical scope across Satomic’s cheminformatics platform. Focused on representation, search, inference, and architectural design: making chemistry queryable. A role where setting direction with incomplete information, choosing the right abstractions, and operating with autonomy are the job. This role is NOT: A pure ML research or model-training position. A medicinal chemistry or synthesis design role. That intuition is helpful, but the work is building the system that serves people working on those challenges. An engineering role with tightly pre-scoped problems, an existing playbook, or a more senior cheminformatics engineer to follow. A role operating in isolation from the rest of engineering. The cheminformatics work sits within the Development team and integrates tightly with the platform's existing systems. You'll have deep ownership of the chemistry search domain, but the surrounding infrastructure — deployment, observability, the broader serving stack — is shared team territory. Qualifications We are looking for an exceptional builder who has skills at the intersection of chemistry, software, and graph search and indexing. If you don’t tick every box below but recognize the shape of the problem, have depth in a combination of these areas, and a track record of learning the third fast and shipping at the edge of your competence, please apply. The intersection is rare by definition– we are looking for the person, not the perfectly formatted resume: 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. You've delivered sub-second p95 for interactive query workloads and sustained high-throughput batch scoring (think 10k+/second), and you know which architectural calls get you there. You think in hot paths, indexing strategies, and inference at scale, and make decisions that survive both growth and change in the underlying domain. Production-level fluency with core cheminformatics tooling (RDKit and/or OpenEye), 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: you have lived with their pains and shortcomings, know where they break, and can 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, and a track record of integrating, extending, or deliberately replacing it. Solid engineering fundamentals with room to grow: Python proficiency required, paired with a genuine enthusiasm for software engineering. We're looking for someone curious about expanding their toolkit and is excited to pick up new languages and explore where different tools shine, whether that's a performance-oriented language like Rust, Go, or C++ or something else entirely. Familiarity with data stores or vector indexes (FAISS, ScaNN, pgvector, or similar) is welcome, though you'll have opportunities to deepen these skills on the job. Most of all, we want someone comfortable reasoning about how their code performs and eager to keep learning. Overview of Satomic's Interview Process 30-minute phone screen: the hiring manager will contact you to schedule a 20 minute call. This will not be a technical evaluation, but provides a chance to discuss the role, Satomic's mission and culture, and answer your early questions. 3 x 45 minute interviews with a member of the chemistry team, the head of Development (technical), and the CEO. 90 minute final round: candidates that are selected for the final round will be given a take-home assignment ahead of time to present and discuss Compensation This role offers a base salary of $180,000-$200,000, along with meaningful equity ownership and competitive benefits. We are an early-stage company and design offers to balance cash compensation and with equity ownership. The salary range above reflects base pay only, and we work with candidates to build a package that aligns with their preferences. Final offers are based on a candidate's experience and expected impact. For candidates exceptionally aligned with the role we are comfortable positioning offers toward the top of this range and beyond.

Responsibilities

Design and build a production-grade chemistry search engine that integrates predictive models and retrosynthesis tooling. Act as the technical owner of the cheminformatics domain, defining architecture and scaling the team over time.