Advisor - Cheminformatics & Computational Chemistry
Eli Lilly and Company
October 15, 2026
Full-time
On-site
US, San Francisco CA
Clinical Research and Development
At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.
Organization Overview
Lilly Catalyze360 is a comprehensive approach to enabling the early-stage biotech ecosystem by democratizing access to infrastructure, expertise, and resources. Through its interconnected pillars—Lilly Ventures, Lilly Gateway Labs, Lilly ExploR&D, and Lilly TuneLab—Catalyze360 strategically removes barriers that traditionally block bold science from becoming life-changing medicines, providing biotechs with flexible combinations of capital, physical lab space, R&D capabilities, AI/ML tools, and decades of enterprise learning.
Lilly TuneLab is an artificial intelligence and machine learning (AI/ML) platform that provides biotech companies access to drug discovery models trained on years of Lilly's research data. Lilly estimates that this first release of AI models includes proprietary data obtained at a cost of over $1 billion, representing one of the industry's most valuable datasets used to train an AI system available to participating companies. By integrating advanced in silico modelling and federated learning, we connect pioneering machine learning algorithms, substantial computational power, exclusive datasets, and Lilly’s domain-specific knowledge to drive innovation in drug discovery and facilitate access to optimal therapies for patients.
Job Summary
We are seeking a highly motivated Cheminformatics/Computational Chemistry Scientist to design, evaluate, and build end-to-end small molecule computational workflows within the TuneLab platform. This role requires strong hands-on expertise in state-of-the-art computational methods across the drug discovery pipeline, from virtual screening to lead optimization.
You will work at the intersection of cheminformatics, physics-based modeling, and machine learning, partnering closely with TuneLab software engineering and ML teams to deliver scalable, production-grade workflows.
This is a high-impact role, where you will independently evaluate tools, make build-vs-buy decisions, and deliver robust workflow solutions.
Key Responsibilities
End-to-End Workflow Development
Design and implement workflows spanning:
Virtual screening (ligand-based and structure-based)
Hit identification and hit expansion
Hit-to-lead selection
Lead optimization
Method Development & Application
Apply and integrate core computational chemistry and cheminformatics methods, including:
Ultra-large library search:
Substructure search
Fingerprint and embedding-based similarity search
Shape and pharmacophore-based screening
Molecular enumeration:
Reaction-based enumeration
Fragment-based design and expansion
Ligand-based modeling:
QSAR, similarity, clustering, active learning loops
Structure-based modeling:
Docking, rescoring, pose prediction, structure-aware search
Physics-based methods:
Free energy perturbation (FEP) and related approaches
Cross-functional Collaboration
Partner with:
Machine Learning teams to integrate predictive and generative models
Software Engineering teams to productionize workflows and ensure scalability
Scientific stakeholders to align workflows with drug discovery needs
Minimum Requirements
PhD in Cheminformatics, Computational Chemistry, or Medicinal Chemistry
2+ years of experience applying computational chemistry methods or tools in small molecule drug discovery, including graduate research
2+ years of hands-on experience with physics-based computational methods (e.g., MD, FEP), including graduate research
Additional Skills/Preferences
Demonstrated expertise in structure-based design or ligand-based modeling
Hands-on experience with computational chemistry tools such as RDKit, Schrodinger Suite, or equivalent
Strong programming skills in Python
Experience with docking platforms (e.g., Glide, AutoDock, GOLD)
Strong understanding of small molecule drug discovery workflows
Experience screening commercial chemical libraries (e.g., Enamine, ZINC), ideally at ultra-large scale
Experience with substructure and similarity search, pharmacophore modeling, or reaction- and fragment-based enumeration
Familiarity with generative or diffusion-based approaches in molecular design
Experience building scalable computational workflows
Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form ( https://careers.lilly.com/us/en/workplace-accommodation ) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.
Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.
Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).
Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$168,000 - $246,400
Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.
#WeAreLilly
Organization Overview
Lilly Catalyze360 is a comprehensive approach to enabling the early-stage biotech ecosystem by democratizing access to infrastructure, expertise, and resources. Through its interconnected pillars—Lilly Ventures, Lilly Gateway Labs, Lilly ExploR&D, and Lilly TuneLab—Catalyze360 strategically removes barriers that traditionally block bold science from becoming life-changing medicines, providing biotechs with flexible combinations of capital, physical lab space, R&D capabilities, AI/ML tools, and decades of enterprise learning.
Lilly TuneLab is an artificial intelligence and machine learning (AI/ML) platform that provides biotech companies access to drug discovery models trained on years of Lilly's research data. Lilly estimates that this first release of AI models includes proprietary data obtained at a cost of over $1 billion, representing one of the industry's most valuable datasets used to train an AI system available to participating companies. By integrating advanced in silico modelling and federated learning, we connect pioneering machine learning algorithms, substantial computational power, exclusive datasets, and Lilly’s domain-specific knowledge to drive innovation in drug discovery and facilitate access to optimal therapies for patients.
Job Summary
We are seeking a highly motivated Cheminformatics/Computational Chemistry Scientist to design, evaluate, and build end-to-end small molecule computational workflows within the TuneLab platform. This role requires strong hands-on expertise in state-of-the-art computational methods across the drug discovery pipeline, from virtual screening to lead optimization.
You will work at the intersection of cheminformatics, physics-based modeling, and machine learning, partnering closely with TuneLab software engineering and ML teams to deliver scalable, production-grade workflows.
This is a high-impact role, where you will independently evaluate tools, make build-vs-buy decisions, and deliver robust workflow solutions.
Key Responsibilities
End-to-End Workflow Development
Design and implement workflows spanning:
Virtual screening (ligand-based and structure-based)
Hit identification and hit expansion
Hit-to-lead selection
Lead optimization
Method Development & Application
Apply and integrate core computational chemistry and cheminformatics methods, including:
Ultra-large library search:
Substructure search
Fingerprint and embedding-based similarity search
Shape and pharmacophore-based screening
Molecular enumeration:
Reaction-based enumeration
Fragment-based design and expansion
Ligand-based modeling:
QSAR, similarity, clustering, active learning loops
Structure-based modeling:
Docking, rescoring, pose prediction, structure-aware search
Physics-based methods:
Free energy perturbation (FEP) and related approaches
Cross-functional Collaboration
Partner with:
Machine Learning teams to integrate predictive and generative models
Software Engineering teams to productionize workflows and ensure scalability
Scientific stakeholders to align workflows with drug discovery needs
Minimum Requirements
PhD in Cheminformatics, Computational Chemistry, or Medicinal Chemistry
2+ years of experience applying computational chemistry methods or tools in small molecule drug discovery, including graduate research
2+ years of hands-on experience with physics-based computational methods (e.g., MD, FEP), including graduate research
Additional Skills/Preferences
Demonstrated expertise in structure-based design or ligand-based modeling
Hands-on experience with computational chemistry tools such as RDKit, Schrodinger Suite, or equivalent
Strong programming skills in Python
Experience with docking platforms (e.g., Glide, AutoDock, GOLD)
Strong understanding of small molecule drug discovery workflows
Experience screening commercial chemical libraries (e.g., Enamine, ZINC), ideally at ultra-large scale
Experience with substructure and similarity search, pharmacophore modeling, or reaction- and fragment-based enumeration
Familiarity with generative or diffusion-based approaches in molecular design
Experience building scalable computational workflows
Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form ( https://careers.lilly.com/us/en/workplace-accommodation ) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.
Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.
Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).
Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$168,000 - $246,400
Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.
#WeAreLilly