Cheminformatics Senior Scientist
South San Francisco, CA
Experience: 0
Category: Scientific & Clinical
Contractor Work Model: Hybrid
Brand: Joulé
Compensation Range: 80.00 - 90.00 Per Hour
Job ID: 349019
Date Posted: 04/10/2026
Shortcut: http://jobs.systemone.com/EeIYZW
Job Title: Senior Scientist: Cheminformatics & Computational Chemistry
Location: South San Francisco, CA (Hybrid; remote considered case-by-case)
Hours: M-F, 8-5
Type: 7-month contract
Compensation: $80 - 90/hr (depending on qualifications)
Overview
The Cheminformatics Senior Scientist will design and implement end-to-end computational workflows to support small molecule drug discovery within the TuneLab platform. This role is ideal for a highly technical scientist who can independently evaluate tools, integrate advanced modeling approaches, and deliver scalable, production-ready solutions. You will operate at the intersection of cheminformatics, physics-based simulation, and machine learning in a fast-moving, high-impact environment.
Responsibilities
- Design and implement end-to-end workflows spanning virtual screening, hit identification, hit expansion, and lead optimization.
- Develop and integrate ligand-based and structure-based modeling approaches, including QSAR, docking, and pharmacophore modeling.
- Execute ultra-large library searches using substructure, similarity, and embedding-based methods.
- Build molecular enumeration pipelines using reaction-based and fragment-based design strategies.
- Apply physics-based simulation methods such as molecular dynamics (MD) and free energy perturbation (FEP).
- Evaluate computational tools and make build-versus-buy decisions for workflow components.
- Collaborate with machine learning teams to integrate predictive and generative models into workflows.
- Partner with software engineering teams to productionize workflows and ensure scalability and performance.
- Align computational strategies with scientific and drug discovery objectives through cross-functional collaboration.
Requirements
Must Have
- PhD or MS in Cheminformatics, Computational Chemistry, Medicinal Chemistry, or a related field.
- Strong understanding of small molecule drug discovery workflows.
- Demonstrated expertise in:
- Substructure and similarity search (fingerprint-, graph-, or embedding-based)
- Shape and pharmacophore screening
- Reaction-based and fragment-based enumeration
- Docking and structure-based design
- QSAR and ligand-based modeling
- Active learning and iterative design strategies
- Physics-based simulations (e.g., MD, FEP)
- Hands-on experience with cheminformatics and modeling tools such as RDKit, OpenEye, or similar.
- Experience with docking platforms (e.g., Glide, AutoDock, GOLD).
- Strong programming skills in Python.
- Ability to work independently and apply scientific judgment to complex problems.
Nice to Have
- Experience working with ultra-large chemical libraries (e.g., Enamine REAL, WuXi Galaxy).
- Familiarity with generative chemistry approaches (SMILES-, graph-, or diffusion-based models).
- Experience integrating machine learning models into production workflows.
- Experience with workflow orchestration tools such as Airflow or Nextflow.
Benefits
System One, and its subsidiaries including Joulé, ALTA IT Services, and Mountain Ltd., are leaders in delivering outsourced services and workforce solutions across North America. We help clients get work done more efficiently and economically, without compromising quality. System One not only serves as a valued partner for our clients, but we offer eligible employees health and welfare benefits coverage options including medical, dental, vision, spending accounts, life insurance, voluntary plans, as well as participation in a 401(k) plan.
System One is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex (including pregnancy, childbirth, or related medical conditions), sexual orientation, gender identity, age, national origin, disability, family care or medical leave status, genetic information, veteran status, marital status, or any other characteristic protected by applicable federal, state, or local law.
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