Senior Cheminformatics Engineer

Job Description

Senior Cheminformatics Software Engineer

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About Ten63 Therapeutics

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Ten63 Therapeutics is focused on improving human health by developing better, more durable therapeutics against cancer and some of the world's most lethal diseases. We are leveraging our proprietary in silico platform BEYOND to generate novel therapeutics to hit previously undruggable targets. We're pioneering an engineered approach to drug discovery by scaling quantum simulations and fusing them with generative chemistry to tackle previously undruggable, high-impact targets. Our team of pioneering scientists, engineers, drug hunters, and quantum chemists values passion, teamwork, out of the box thinking and determination to solve even what seems impossible. We embrace diversity and are committed towards inclusion.

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Position Overview

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We are seeking an exceptional Senior Scientific Software Engineer to join our team of pioneering scientists, engineers, drug hunters and quantum chemists. This role is for a builder: someone fluent in cheminformatics and computational chemistry whose primary craft is software engineering. You will take programs that begin life as notebooks and one-off scripts and turn them into tested, versioned, documented production systems that our drug hunters depend on every day. You will own the software layer of our BEYOND platform — the cheminformatics libraries, workflow orchestration, data models, APIs, and internal tools that let computational and medicinal chemists work at scale without babysitting infrastructure.

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A significant part of this role is making powerful computational methods feel obvious to the scientist using them. If you have designed interfaces for molecular modeling software — the 3D viewers and structure-based design environments that chemists live in, such as PyMOL, ICM from MolSoft, Maestro, MOE, or an in-house equivalent — we are especially interested in talking with you.

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Key Responsibilities

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• Own the cheminformatics core: the production Python behind molecular standardization, descriptors and fingerprints, filtering, conformer generation, docking, and property prediction — along with the tests, CI, packaging, profiling, and release discipline that keep it dependable as it grows
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• Turn methods into products: work with computational chemists, quantum chemists, and ML scientists to move a prototype from notebook to versioned, documented service with a clean API and real users, acting as the technical bridge that keeps tradeoffs legible to engineers and chemists alike
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• Run chemistry at scale: orchestrate high-throughput workflows across SLURM and cloud — submission, monitoring, checkpointing, retries, provenance, cost — on top of data models for compounds, structures, conformer ensembles, poses, trajectories, interaction fingerprints, and assay results that stay reproducible months after the run
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• Build what chemists actually touch: internal web applications and interactive 3D visualization for pose and structure inspection, protein-ligand interactions, and SAR triage, designed so a medicinal chemist gets the answer without learning the pipeline
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• Keep the platform observable and pleasant to work in: logging, metrics, and alerts that catch a failing job before a chemist does, plus the CLIs, project templates, and documentation that lower the cost of good science for everyone else on the team
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Required Qualifications

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• MS or PhD in Computational Chemistry, Chemistry, Chemical Engineering, Computer Science with a chemistry focus, Bioinformatics, or a related field — or a BS with equivalent industry experience — plus 5+ years building and maintaining scientific software that other people rely on in production
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• Expert-level Python and the design judgment behind it: interfaces others can build on, sane concurrency, a deliberate testing strategy, and systematic debugging — the difference between a system and a pile of scripts
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• A concrete record of productionizing research code: specific prototypes you carried through to maintained software with tests, CI, documentation, and releases, and owned end to end from architecture through deployment and long-term maintenance
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• A strong understanding of how python, javascript/typescript, APIs, SQL, Linux and Bash are used in Cheminformatics workflows
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• Cheminformatics and structure-based design fluency: RDKit, molecular file formats (SMILES, SDF, MOL2, PDB, mmCIF), descriptors, fingerprints, substructure and similarity searching, standardization of tautomers, protonation states and salts, and enough SBDD (protein-ligand interactions, docking, scoring, pharmacophores) to reason about 3D structure unaided
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• Fluency in the environment this work lives in: Linux and bash, HPC job schedulers such as SLURM, Git-based collaboration with code review and CI, and SQL and schema design for scientific data
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• Communication that closes the loop with scientists: gathering requirements from bench and computational chemists and turning them into technical specifications and roadmaps they recognize as their own
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• Passion for solving seemingly impossible problems and strong problem-solving skills at the intersection of chemistry, software engineering, and product design
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Preferred Qualifications

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• Interface design for molecular modeling software — PyMOL, ICM from MolSoft, Maestro, MOE, Flare, or something you built in house, with real opinions about 3D manipulation, selection semantics, SAR triage, and making an information-dense screen legible; Figma or comparable prototyping and design-system experience welcome
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• Full-stack delivery of scientific tools: TypeScript with React or Vue over FastAPI, Flask, or Django, and molecular visualization in the browser with 3Dmol.js, NGL, Mol*, or WebGL/Three.js
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• The infrastructure to run it: Docker and Kubernetes, workflow orchestration (Airflow, Prefect, Nextflow, Snakemake, Dask, Ray), and cloud platforms with object storage and infrastructure as code
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• Making slow things fast and hard things unattended: performance work in C++, Rust, Cython, or Numba, and wrapping simulation and quantum chemistry engines (OpenMM, AMBER, GROMACS, Psi4, ORCA, xtb) into automated pipelines
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• Chemistry data and ML in production: compound registration, ELN/LIMS integration, public and commercial libraries (ChEMBL, PubChem, ZINC, Enamine REAL), virtual screening, free energy or ADMET campaigns at scale, and model packaging, serving, and experiment tracking (MLflow, Weights & Biases)
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• Evidence of range: open-source contributions to cheminformatics, molecular modeling, or scientific computing, or a startup where you owned the full stack because nobody else was going to
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Technical Skills

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• Languages and scientific computing: expert Python (NumPy, SciPy, pandas, scikit-learn), Javascript, and C++ at minimum
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• Cheminformatics and molecular modeling: RDKit, Open Babel, ProLIF, or CDK; PyMOL, ICM, or VMD including scripting and extension development; OpenMM, AMBER, GROMACS, Psi4, or ORCA as integration targets
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• Engineering practice and tooling: pytest, type checking, linting, CI/CD, packaging, semantic versioning, Git, Docker, and environment management with conda, pip, or uv
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• Services and interfaces: FastAPI, Flask, or Django; REST and GraphQL API design; React or Vue; 3Dmol.js, NGL, or Mol* for molecular visualization
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• Data and compute: PostgreSQL, SQLite, SQL, and chemical registration schemas; Airflow, Prefect, Nextflow, Dask, or Ray; SLURM and high-performance computing; AWS, GCP, or Azure with object storage
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• Linux/Unix environments and bash scripting
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What We Offer

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• Opportunity to work on previously undruggable targets and fundamentally change the paradigm of drug discovery
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• Collaborative environment with world-class scientists, engineers, drug hunters, and quantum chemists
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• Competitive compensation package including equity and an annual bonus
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• Comprehensive health, life, short- and long-term disability insurance policies
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• 401K matching
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• Access to cutting-edge computational resources and our proprietary BEYOND platform
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• Professional development opportunities
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Ten63 Therapeutics is an equal opportunity employer. We embrace diversity and are committed towards inclusion. We encourage applications from all qualified candidates regardless of race, color, religion, sex, national origin, age, disability, or any other protected characteristic.