Computational Chemist - Drug Discovery & Machine Learning

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.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.  The anticipated wage for this position is

Computational Chemist – Drug Discovery & Machine Learning

DICE Therapeutics, a wholly owned subsidiary of Eli Lilly & Co., is an organization within Lilly Research Labs, a small molecule drug discovery organization with responsibilities spanning from target identification to candidate selection for clinical studies. We are looking to grow our diverse team of scientists. The Computational Chemistry and Cheminformatics (C3) group in DICE is seeking a drug-hunting expert with experience applying advanced computational technologies to real-world molecular design, who can operate across the computational and medicinal chemistry fields to make our drug discovery engine faster and more powerful.

About the Role

We are seeking a highly skilled Computational Chemist with expertise in drug discovery, molecular modeling, and machine learning (ML) to join our research team. This role focuses on applying innovative computational techniques to accelerate small-molecule drug discovery through AI-enabled molecular simulations and predictive modeling. The ideal candidate will work closely with medicinal chemistry, structural biology, biology, and DMPK teams to integrate computational and experimental insights.

Apply now to join our team as a Computational Chemist and drive innovation in drug discovery!

Key Responsibilities

• Apply molecular modeling techniques to support small-molecule drug discovery.
• Develop and implement predictive models for small-molecule properties, docking scores, and ADMET predictions.
• Investigate protein conformations and dynamics using molecular dynamics (MD) simulations, Markov models, enhanced sampling, network analysis, and AI-enabled conformational analysis.
• Design and maintain in silico screening pipelines for ultra-large virtual screening.
• Collaborate with cross-functional teams to interpret experimental data, refine computational strategies, and enhance biophysical insights.
• Stay up to date with advancements in ML-driven drug discovery, cheminformatics, and computational chemistry.

Basic Qualifications

• Ph.D. in Computational Chemistry, Theoretical Chemistry, Biophysics, Bioinformatics, or a related field.
• 0-2+ years of experience in computational chemistry, machine learning, or drug discovery research.

Preferred Skills & Experience

• Expertise in protein-ligand modeling, molecular dynamics (MD) simulations, and free energy calculations.
• Knowledge of enhanced sampling techniques (e.g., Metadynamics, Umbrella Sampling) and AI-enabled molecular simulations.
• Hands-on experience with ML models for molecular property / ADME prediction.
• Experience with molecular modeling tools (e.g., Schrödinger, MOE, NAMD, GROMACS), ML libraries (e.g., TensorFlow, PyTorch, scikit-learn), and Cheminformatics tools (e.g., RDKit, DeepChem).
• Proficiency in scripting (Python, Bash) and data analysis (Spotfire or similar).
• Familiarity with biophysical techniques (e.g., cryo-EM, NMR, SPR, ITC, X-ray crystallography) is a plus.
• Experience with high-performance computing (HPC) and cloud computing.
• Strong communication, collaboration, and problem-solving skills in a multidisciplinary team environment.

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Our employee resource groups (ERGs) offer strong support networks for their members and help our company develop talented individuals for future leadership roles. Our current groups include: Africa, Middle East, Central Asia Network, African American Network, Chinese Culture Network, Early Career Professionals, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinos at Lilly, PRIDE (LGBTQ + Allies), Veterans Leadership Network, Women’s Network, Working and Living with Disabilities. Learn more about all of our groups.

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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