Post-doctoral Computational Chemist, Advanced Molecular Design

Eli Lilly and Company • Indianapolis, IN

6d • $58,000 - $123,200 • 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 hit identification 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.
• 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.
• Demonstrated experience with reproducible code practices and version control (GitHub/GitLab).
• Strong interpersonal, organizational, and problem-solving skills.

Nice To Haves

• Develop deep working knowledge of computational chemistry suites including Schrödinger, MOE, Gaussian/Orca/GAMESS, and one or more MD packages (OpenMM, AMBER, CHARMM, GROMACS, or Desmond).
• 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.
• Experience integrating structural biology data (cryo-EM, X-ray crystallography, NMR or AI-predicted structures) into computational design workflows.

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 for 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
• 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
• 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