Post-doctoral Computational Chemist, Advanced Molecular Design

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.

Post-doctoral Computational Chemist
Location: Indianapolis, Indiana, United States of America

We serve an extraordinary purpose. For 150 years, we have worked diligently to discover medicines that make life better. These discoveries start in Lilly Research Laboratories, where our scientists work to create new medicines that will help solve our world's greatest health challenges. We are looking for a highly motivated Postdoctoral Computational Chemist to join our Advanced Molecular Design (AMD) team within Lilly Research Labs, Indianapolis, Indiana.

AMD applies cutting-edge computational methods to accelerate drug discovery across Lilly's portfolio. Our team integrates structure-based design, quantum mechanics, molecular dynamics, free energy calculations, and AI/ML approaches to advance molecules from hit identification through clinical candidate selection.

• 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 enabling 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.
• 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).
• 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.

• Ph.D. in Computational Chemistry, Computer Science, Cheminformatics, Bioinformatics, Biophysics or 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
• 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, Open Eye) or structural analysis platforms (Schrodinger, Chem Axon)
• Proficiency in scientific computing libraries and APIs (MD Analysis, Num Py, Sci Py, pandas) beyond basic scripting
• Ability to build and automate computational workflows with minimal supervision
• Demonstrated…