Skip to main content

This job has expired

You will need to login before you can apply for a job.

Advisor / Sr. Advisor - ML/AI Protein Design Scientist

Eli Lilly and Company
San Diego, California
Start date
May 9, 2024

View more

Science/R&D, Biotechnology
Required Education
Position Type
Full time
Biotech Beach, Best Places to Work

Job Details

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.

The Biotechnology Discovery Research Division in San Diego plays a crucial role in generating, characterizing, and optimizing biotherapeutics, from hit generation through lead optimization and preclinical development. We support cross-disciplinary efforts to engineer innovative biotherapeutics that treat metabolic, autoimmune, oncologic, and neurologic diseases.

We are currently seeking a self-motivated, collaborative Machine Learning Scientist to drive ML/AI powered protein design for next-generation biologics, including antibody, protein, peptide and beyond.  If you are an expert in machine learning and a relentless problem solver who shares our passion for making a difference, we invite you apply!


  • Design and implement cutting-edge algorithms, such as diffusion or LLM -based protein models, for de novo protein design.

  • Develop in silico or de novo antibody discovery and engineering methods to enable challenging targets.

  • Analyze diverse experimental data, identify gaps in model capabilities, and enhance the performance of the protein design pipeline.

  • Evaluate and push the boundaries of state-of-the-art algorithms, particularly those related to protein design.

  • Partner with experimental, computational scientists, and IT professionals to refine strategies for data generation and acquisition for ML trainings.

  • Regularly share progress in internal and cross-functional research meetings. Additionally, actively engage with the external scientific community by contributing through publications and presentations.

Basic qualifications

  • PhD in computational biology, computer science, bioinformatics, or a related discipline.

  • Industry Experience developing and applying machine learning and AI algorithms addressing protein design and engineering problems of biological interest.

Preferred qualifications:

  • Proficiency in programming languages/tools (Python or R).

  • Hands-on experience with RosettaFold, RFdiffusion, AlphaFold, or ESM, ESMFold.

  • Proficiency in protein modeling and design software, such as PyMOL, Rosetta, Schrodinger, Molecular Operating Environment (MOE).

  • Strong publication record in protein design and engineering for therapeutic proteins. Experience with antibodies highly desired.

  • Excellent written and oral communication skills, including an ability to explain complex ideas to partners (e.g. experimentalists, data scientists, and other computational scientists/IT professionals).

  • Understand business requirements and effectively translate business needs and process into technical terms, and vice versa.

  • Strong collaborative skills and proven ability to work with a cross-functional team.

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.

Lilly is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status.

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.



Science has been our calling from the beginning. Colonel Eli Lilly founded the company in 1876 and charged employees to “take what you find here and make it better and better.” More than 147 years later, we remain committed to his vision through every aspect of our business and the people we serve, starting with discovering the best treatments for those who take our medicines and extending to health care professionals, employees and the communities in which we live. Moreover, you can also count on the team at Lilly to be incredibly civic-minded, supporting our communities through philanthropy, volunteerism, and a creative and innovative can-do spirit. 

Company info
893 S Delaware St
United States

Get job alerts

Create a job alert and receive personalized job recommendations straight to your inbox.

Create alert