Director / Senior Director - Cheminformatics and Applied AI

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.

Overview

At Lilly, we serve an extraordinary purpose. We make a difference for people around the globe by discovering, developing, and delivering medicines that help them live longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism. The Lilly Small Molecule Discovery is an organization purpose-built to create molecules that make life better for people. We focus on using cutting edge science to unlock new approaches that can treat people suffering from diseases with poor treatment options. We continually challenge ourselves to deliver molecules that can provide breakthrough efficacy with the highest possible safety margins. We are dedicated to optimizing our mindset, technology, and processes for faster, more nimble execution. Our success is built on a culture that empowers innovative problem solving through open collaboration and individual accountability.

Position Summary

Lilly’s Early Molecule Discovery (EMD) mission is to identify hits and deliver optimized Leads that advance though Advanced Molecule Design (AMD) into quality drug candidates and, ultimately, breakthrough medicines. The primary measure of success in this band is portfolio-level impact — resolving the hardest scientific questions through hypothesis- and data-driven approaches, delivering the insights that change the trajectory of multiple programs, and building the scientific capabilities that raise the ceiling on what the function can achieve. The Director/Senior Director of Cheminformatics and Applied AI are recognized scientific authorities whose impact extends well beyond individual projects to define platform capabilities, shape discovery strategy, and advance the state of the art within Lilly and across the field. These are not primarily execution roles — they are roles of scientific vision, organizational leadership, and enterprise influence.

Key Responsibilities

• Portfolio Impact: Scientific leadership through direct technical credibility Serve as a recognized expert in cheminformatics and applied AI/ML, who consistently delivers high-impact scientific contributions and strategies that resolve critical project challenges to advances programs through major milestones.
• Develop and apply cheminformatics, statistical, and AI/ML methods that improve hit identification and hit-to-lead across screening technologies, e.g., DNA-encoded library (DEL), high-throughput screening (HTS), virtual screening (VS), fragment-, and affinity-based approaches, and across modalities, e.g., small molecule, macrocyclic peptide, and molecular glues.
• Drive the analytical and machine learning methodology development and applications for the DEL platform: enrichment analysis and denoising of selection data, models trained on DEL output, and their extension to VS of ultra-large synthesizable chemical space.
• Identify hard scientific problems limiting program progress and take personal ownership of driving solutions through rigorous and creative scientific thinking.
• Stay current with external scientific advances, emerging methodologies, techniques, and enabling technologies and rapidly evaluate, adapt, and deploy those most relevant for advancing program objectives.
• Enabling: Scientific Influence and Strategic Partnerships Partner with Computational Chemistry and Cheminformatics leadership to define platform-level strategy, resource investments, and organizational priorities for Cheminformatics and Applied AI. Encourage close collaborations and initiatives with computational chemistry, medicinal chemists, Ligand-ID, Biophysics and Chemical Biology cross pillar colleagues and other cross function partners such as ADME, that culminate in the generation of well poised analysis, robust models and testable hypotheses. Serve as a scientific advisor to senior leadership across discovery, therapeutic areas, and technical functions; provide expert guidance across multiple programs; influence portfolio-level decisions through authoritative scientific judgment. Identify and contribute to external innovation opportunities that enhance our ability to deliver quality differentiated hits and leads. Build and leverage external scientific networks e.g. academic collaborators, CROs, technology vendors, professional societies, to access groundbreaking scientific expertise and capabilities. Cultivate cross function collaborations with Discovery & Technology Platforms and View email address on click.appcast.io colleagues to help guide the delivery of transformative digital solutions. Foster an environment that supports open scientific debate and bold, evidence-based decisions; champion integration of complementary fields to improve translational impact across the discovery continuum.
• Supporting: Team Development and Culture Serve as a role model for scientific excellence at all levels of the organization; establish clear expectations for rigor, independence, innovation, and measurable impact. Actively mentor and develop diverse scientific talent across sites and functions; develop team members' ability to deliver higher-impact science and reinforces curiosity; invest in building the next generation of scientific leaders. Challenge the status quo; Lead complex (cross-functional) initiatives that leverage diverse perspectives, to drive improvement, and accelerate adoption of new scientific approaches. Champion a ONE TEAM, SAME TEAM mindset; exemplify Lilly leadership behaviors and model ground-breaking transparency in surfacing issues that detract from our mission to accelerate the delivery of our portfolio.
• Safety & Compliance: Model Safety Leadership Through Personal Practice Demonstrate an unwavering commitment to safety-first practice: complete required safety training and raise concerns immediately. Follow all site safety, environmental, and regulatory compliance requirements; actively reinforce a non-negotiable safety-first team culture and drive solution of concerns at the appropriate organizational level.

Basic Requirements

PhD in Cheminformatics, Computational Chemistry, Chemical Engineering or related field with a minimum of 4+ years of drug discovery experience within a pharmaceutical/biotech setting; or BS/MS with 8+ years of equivalent experience.

Additional Preferences

Proven ability to provide scientific leadership that shapes organizational capabilities, scientific culture, and strategic direction at the project, platform, and/or portfolio level. Demonstrated drug-hunter experience with a track record of successfully developing, applying, and championing (new) cheminformatics and applied AI/ML technologies to advance discovery programs through major milestones, such as hit ID, hit-to-lead progress. Broad understanding of modern data science applied to drug discovery, including predictive modeling, generative design, molecular representations, and model validation and uncertainty. Proficiency in Python and SQL, cheminformatics toolkits (RDKit, OpenEye), and machine learning libraries (PyTorch, scikit-learn). Fluency with AI coding and research assistants such as Claude Code. Proven ability to inspire and collaborate with scientists across teams and functions to achieve aspirational goals with demonstrated translation to drug discovery outcomes. Exceptional track record of scientific innovation evidenced by publications, patents, invited presentations, or other indicators of field-level recognition and external scientific impact. Outstanding written and verbal communication skills, with demonstrated experience presenting to and influencing senior scientific and business leadership. Data dependent decision maker; agile and ready to change research priorities as necessary for success. Demonstrated interest in building inclusive teams and commitment to mentoring early career computational chemists. Domain expertise in target classes and modalities aligned with Lilly’s strategic interests. Project or program leader experience. Excellent understanding of the phases of drug discovery from target assessment through to candidate selection and the fundamental concepts of drug design, medicinal chemistry and ADME.

Physical Demands / Travel

The physical demands here are representative of those that must be met by an employee to successfully perform the essential functions of this job. There will be some travel associated with this role.

Work Environment

This is an onsite office position within Lilly Research Laboratories. The work environment characteristics described here are representative of those an employee encounters while performing the essential functions of this job. To perform this job successfully, an individual must be able to perform the role and responsibilities satisfactorily. The requirements listed above are representative of the knowledge, skill, and/or ability required. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions.

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 ( 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 (View email address on click.appcast.io), 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 $193,500 - $308,000. 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 At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe! #WeAreLilly