Post-doctoral Computational Chemist, Advanced Molecular Design

Eli Lilly and Company • Us, IN

3d • Onsite

About The Position

Lilly is seeking a highly motivated Postdoctoral Computational Chemist to join its Advanced Molecular Design (AMD) team within Lilly Research Labs in Indianapolis, Indiana. The AMD team utilizes state-of-the-art computational methods to accelerate drug discovery across Lilly's portfolio. This role involves integrating various computational approaches, including structure-based design, quantum mechanics, molecular dynamics, free energy calculations, and AI/ML, to advance molecules from initial discovery through to clinical candidate selection. The successful candidate will contribute to developing and applying computational methods to speed up the discovery of new medicines within a collaborative and innovative scientific environment.

Requirements

• Ph.D. in Computational Chemistry, Computer Science, Cheminformatics, Bioinformatics, Biophysics or a related field with all completed requirements by August 2026.
• 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.

Nice To Haves

• Strong foundation in theoretical physical chemistry and organic chemistry.
• Experience with molecular dynamics simulations, quantum mechanical or free energy calculation methods applied to protein-ligand systems.
• Proficiency in Python and other scripting and programming languages.
• Ability to work effectively both independently and in a collaborative team environment.
• Knowledge of lead optimization using structure-based design and AI/ML models.
• Familiarity with ADME and toxicology concepts in the context of drug discovery.
• Experience working on HPC environment.
• Experience with cheminformatics toolkits (RDKit, OpenEye) or structural analysis platforms (Schrodinger, ChemAxon).
• Proficiency in scientific computing libraries and APIs (MDAnalysis, NumPy, SciPy, pandas) beyond basic scripting.
• Ability to build and automate computational workflows with minimal supervision.
• Demonstrated experience with reproducible code practices and version control (GitHub/GitLab).
• Experience integrating structural biology data (cryo-EM, X-ray crystallography, NMR or AI-predicted structures) into computational design workflows.
• Strong interpersonal, organizational, and problem-solving skills.

Responsibilities

• Develop and apply computational methods to accelerate the discovery of new medicines.
• Execute advanced quantum mechanical calculations, molecular dynamics simulations, and free energy calculations to study protein motion, protein-ligand interactions, and protein-protein interactions in support of structure-based drug design.
• Build and maintain informatic infrastructure to enable broad utilization of quantum mechanics, molecular dynamics, and free energy methods across drug discovery projects.
• Script and automate workflows across computational software platforms to maximize throughput and reproducibility of molecular calculations.
• Stay current with emerging methods in computational drug discovery, including AI and machine learning models for molecular property prediction and design.
• Work as part of a multidisciplinary team, including medicinal chemists, structural biologists, biologists, statisticians, and toxicologists, to deliver computational insights that advance drug discovery projects.
• Maintain critical timelines and communicate progress clearly through oral and written presentations at internal and external team meetings.
• Collaborate with discovery scientists to advance portfolio molecules from leads to quality drug candidates.

Benefits

• company bonus (depending, in part, on company and individual performance)
• company-sponsored 401(k)
• pension
• vacation benefits
• medical benefits
• dental benefits
• vision benefits
• prescription drug benefits
• flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts)
• life insurance
• death benefits
• certain time off and leave of absence benefits
• well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

What This Job Offers

• Job Type: Full-time
• Career Level: Entry Level
• Education Level: Ph.D. or professional degree