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Eli Lilly and Company | EMD C3 – Early Molecule Discovery
Position Overview
Eli Lilly’s EMD C3 (Computational Chemistry & Cheminformatics) group is seeking a Postdoctoral Scientist to advance Synth(on)-Fragment–based Virtual Screening (SFBVS) for early small-molecule drug discovery. This role focuses on developing synthesis-aware virtual screening workflows that connect fragment-level binding hypotheses to synthesizable chemical space, lowering barriers to synthesis and accelerating hit discovery.
The position offers a unique opportunity to work at the intersection of AI, structure-based drug design, fragment chemistry, and synthesis, contributing directly to Lilly’s next-generation virtual screening capability.
Key Responsibilities
- Develop and apply synth(on)-fragment–based virtual screening methods for small-molecule hit discovery.
- Design fragment growth, linking, and merging strategies constrained by real-world synthetic feasibility.
- Integrate structure-based modeling (docking, scoring, ML/DL affinity prediction) with reaction-aware generative designs.
- Prioritize compounds that balance binding potential, chemical diversity, and synthetic accessibility.
- Collaborate closely with medicinal chemists, fragment scientists, and screening teams to enable rapid experimental validation.
- Apply workflows to novel and challenging EMD targets, including difficult or underexplored pockets.
Basic Qualifications
- PhD in Computational Chemistry, Computer Science, or a related field.
- Strong background in CADD and structure-based drug design.
- Experience with fragment-based drug discovery concepts.
- Proficiency in Python and familiarity with cheminformatics tools (e.g., RDKit).
- Proficiency in DL/ML methods for binding prediction or molecular design.
- Ability to work with large chemical libraries and computational workflows.
- Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1.
Preferred Qualifications
- Experience with synth(on)- or reaction-based chemical libraries.
- Familiarity with synthetic accessibility scoring, retrosynthesis, or reaction rule systems.
- Experience collaborating with medicinal chemistry teams.
- Strong collaboration and scientific communication skills.
Why Join Lilly EMD C3
- Contribute directly to high prioritity small-molecule discovery programs.
- Help define scalable, synthesis-aware virtual screening strategies.
- Work in a highly collaborative, multidisciplinary AI-driven environment.
- Access industry-leading compute, data, and experimental platforms.
Additional Information:
- The position is located at Seaport. Innovation Center, Boston.
- Onsite working model.
- This position is not permanent. It is for a fixed term position up to a maximum of 4 years.
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Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is
$58,000 - $123,200
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.
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