Post-doctoral Computational Chemist, Advanced Molecular Design

About the role

The successful candidate will join an interactive, collaborative, and innovative scientific team to develop and apply computational methods that accelerate the discovery of new medicines. They will 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. They will script and automate workflows across computational software platforms to maximize throughput and reproducibility of molecular calculations. They will 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).

Responsibilities

• 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.
• 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.

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.

Qualifications

• 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.
• 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.

Skills/Preferences

• Experience with AI and machine learning models for molecular property prediction and design.
• Experience 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.
• 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.

Benefits

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).

Pay

The anticipated wage for this position is $58,000 - $123,200

Schedule

This is an onsite position based in Indianapolis, Indiana