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Lilly Advisor - Structure Based Drug Design in San Diego, California

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 35,000 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.

At Lilly, we serve an extraordinary purpose. We make a difference for people around the globe by discovering, developing and delivering medicines that help them live longer, healthier, more active lives. Not only do we deliver breakthrough medications, but you also can count on us to develop creative solutions to support communities through philanthropy and volunteerism.

The Discovery Chemistry Research and Technologies (DCRT) organization within Lilly Research Labs is 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 DCRT is seeking a computational scientist. You should have demonstrated experience in applying computational techniques in small molecule structure-based design, particularly in utilization of free energy methods and molecular dynamics in hypothesis creation.

Do you have experience using artificial intelligence/machine learning (AI/ML) for design and development of potency models and generative design of compounds? This is the perfect opportunity for you. Apply today and join the Lilly family working together to bring life changing medicines to patients!

Some responsibilities in this role:

  • Generate computational models to help direct synthetic strategies, idea generation and prioritization.

  • Use advanced computational techniques to study protein motions, protein-ligand interactions, or protein-protein interactions to understand binding and enable structural design of new molecules.

  • Apply computational techniques such as conformational analysis, structure searches, docking, molecular dynamics simulations, homology modeling, pharmacophore modeling, free energy perturbation, machine learning, virtual screening and advanced data analytics to solve medicinal chemistry research problems.

  • Collaborate in a multidisciplinary team of medicinal chemists, structural biologists, biologists, statisticians and toxicologists to provide computational expertise to advance drug discovery projects.

  • Champion broad utilization of free energy methods across discovery projects.

  • Perform large scale data extraction, manipulation, and merging of multiple data sets for statistical analysis and scoring to understand structure activity relationships.

  • Script workflows in various computational software to efficiently perform molecular calculations.

  • Develop a deep understanding and practical, working knowledge of software suites such as MOE, Schrodinger, CHARMM, AMBER, Cresset, Knime, ChemAxon, Macromodel, and Gaussian to apply to computational research.

  • Contribute to the development of desktop applications for medicinal chemists by developing scripts or workflows for efficient use of software and subsequent training of workflows.

Basic Qualifications

PhD in Computer Science, Cheminformatics, Computational Chemistry, Bioinformatics or related field

Additional Skills/Preferences

  • Potential to develop project-level focus and ability to influence across multiple functions

  • Interest in potency, ADMET parameters, and multi-parameter optimization and how to incorporate them into molecular design

  • Hands on experience in use of free-energy perturbation methods and molecular dynamics

  • Experience in scripting or programming languages such as Python, Perl, or C/C++.

  • Strong oral and written communication skills

Eli Lilly and Company, Lilly USA, LLC and our wholly owned subsidiaries (collectively “Lilly”) are committed to help individuals with disabilities to participate in the workforce and ensure equal opportunity to compete for jobs. If you require an accommodation to submit a resume for positions at Lilly, please email Lilly Human Resources ( ) for further assistance. Please note This email address is intended for use only to request an accommodation as part of the application process. Any other correspondence will not receive a response.

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As a condition of employment with Eli Lilly and Company and its subsidiaries in the United States and Puerto Rico, you must be fully COVID-19 vaccinated and provide proof of vaccination satisfactory to the company (subject to applicable law).