Advisor - Fragment-based Computational Design

Company: Eli Lilly and Company
Location: San Francisco
Posted on: June 24, 2025

Job Description:

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world. 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. Discovery Technology and Platforms is a newly established function within this organization. Its mission is to accelerate molecule discovery by building highly optimized foundational platforms, streamlining lab operations through advanced technologies and data connectivity, and intentionally investing in novel technologies and capabilities. About the Novel Platforms Team The Novel Platforms team identifies and develops transformative technologies to improve hit finding, mechanism of action exploration, and molecular design. Through agile, hypothesis-driven research, we turn high-potential ideas into mature, robust platforms embedded across Lilly’s discovery organization. Position Summary Lilly Small Molecule Discovery is seeking a Computational Scientist to join our Novel Platforms Fragment-based Discovery team. We are reimagining Fragment-Based Lead Discovery (FBLD) by embedding computation at its core—from data curation and modeling to design, triage, and decision-making. You will be a key contributor to an interdisciplinary initiative spanning structural biology, biophysics, chemistry, and AI systems, with the mission of transforming how fragments are discovered, evolved, and optimized. You’ll develop and integrate cutting-edge tools, to extract insight from diverse experiments—SPR, NMR, crystallography, cryo-EM, virtual screens—and convert them into actionable hypotheses. Your work will directly impact how Lilly identifies, and advances leads against challenging targets. Key Responsibilities Scientific & Technical Leadership Utilize state-of-the-art software to grow, link and merge fragment hits into novel chemical designs as well as work with informaticians to develop novel methods to improve this process. Triage and extract key pharmacophoric and structural insights from early biophysics and fragment screening data. Build and improve on internal proprietary fragment libraries and develop bespoke cassette relevant to the target class being explored Coordinate with internal and external chemistry resources to prioritize and ensure timely delivery of the chemical matter. Collaborate closely with biophysicists, structural biologists, medicinal chemists, and AI discovery teams. Innovation & External Awareness Stay at the forefront of computational FBLD innovations, AI-enhanced design, and in silico fragment evolution. Evaluate and integrate best-in-class tools, open-source frameworks, and academic advancements. Drive tool adoption and best practices in fragment modeling and AI-integrated design. Required Qualifications Ph.D. with 3 years or M.S. with 5 years of industry experience in structural biology, chemical biology, or related fields. Hands-on experience with software pertaining to FBLD such as Maestro/Schrodinger, ICM-Pro, GINGER, FrankenROCS, Fragmentstein, cluster4x, PanDDA, and the use of scripting to automate their use, ideally in a High-Performance Computing (HPC) environment. Proven track record of FBLD. Proven ability to independently design experiments, troubleshoot challenges, and effectively collaborate in a fast-paced environment. Additional Preferences: Hands-on experience with biophysical assays for protein characterization, binding analysis and Molecular Dynamics (MD). Experience in X-ray crystallography and cryo-EM data collection, processing, protein model and ligand building. Experience in developing methods to identify ligand-ready cryptic pockets. Passion for platform development, continuous optimization, and operational excellence with a strong emphasis on data quality and reproducibility. Adaptability and resilience in a fast-paced, evolving research environment. Additional Information Physical Demands/Travel: The physical demands of this job are consistent with a laboratory environment . This position will require 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. Work Environment: This position’s work environment is in a laboratory. 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 ( 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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups. Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $156,750 - $250,800 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

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