Advisor - Protein Engineering (Biotechnology Discovery Research)

Position Overview

At Lilly, we unite caring with discovery to make life better for people around the world. As a global healthcare leader, Lilly is dedicated to discovering and delivering life-changing medicines. The Biotechnology Discovery Research group at Lilly’s Biotechnology Center in San Diego is looking for a highly motivated scientist with expertise in protein engineering/biochemistry and/or structural biology to support and lead efforts in designing, engineering, and optimizing protein therapeutics that improve biological function, stability, and developability. This role collaborates with interdisciplinary teams to advance innovative research and make a difference for patients and communities.

Key Responsibilities

• Design, engineer, and optimize novel protein therapeutics using structure-guided and experimental/library approaches to enhance biological function, potency, time-action, stability, and immunogenicity profiles.
• Apply knowledge of protein structure–function relationships and structure–activity relationships (SAR) to guide molecular engineering efforts.
• Lead independent research projects from concept to execution, including critical analysis of experimental results and strategy development for novel biotherapeutics.
• Troubleshoot complex challenges in protein engineering and develop innovative solutions.
• Advance core capabilities in antibody and protein engineering and contribute to the development of new platform technologies.
• Serve as a protein engineering lead on cross-functional project teams, collaborating with experts in computational biology, development, manufacturing, and translational teams.
• Present research findings at internal meetings and contribute to scientific publications and regulatory documents as appropriate.
• Mentor junior scientists and research associates to support their technical development and career growth.
• Stay current with emerging scientific trends and maintain awareness of the competitive landscape in biologics discovery.

Required Qualifications

• Ph.D. in protein engineering, protein biochemistry, structural biology, protein biophysics, molecular biology, or a related field.
• Strong foundation in protein structure and function with proven success in applying rational protein design and experimental approaches in engineering affinity, function, or stability.
• Proficiency in computational tools for structure modeling and analysis (e.g., Rosetta, Schrödinger, Chimera, PyMOL, MOE, AlphaFold).
• Hands-on experience in molecular cloning and protein engineering.

Preferred Qualifications

• Postdoctoral or industry experience in protein engineering or structural biology.
• Basic proficiency in Python and/or R for data analysis, workflow automation, or integration with bioinformatics tools.
• Proven track record of scientific productivity (e.g., first-author publications, patents, or conference presentations).
• Excellent analytical and problem-solving skills with great attention to detail.
• Effective written and verbal communication skills and a collaborative, team-oriented mindset.
• Comprehensive knowledge in protein sciences such as cloning, expression, purification, characterization, structural biology, protein–protein interactions, and SAR.
• Hands-on experience in library design and screening (e.g., phage or yeast display).
• Understanding of antibody generation and biologics drug discovery research.
• Exposure to AI or machine learning approaches in protein design is a plus.
• Commitment to diversity, equity, and inclusion in the workplace.
• Desire and commitment to continuous learning.
• Ability to thrive in a fast-paced, dynamic research environment with strong organizational and multitasking skills.
• Ability to effectively partner with cross-functional colleagues across geographies.
• Proficiency with scientific software (e.g., Spotfire, JMP) and Microsoft Office applications.

Benefits & Perks

• Compensation: Anticipated wage range of $138,000 - $224,400. Actual compensation depends on education, experience, skills, and geographic location.
• Full-time employees are also eligible for a company bonus based on performance.
• Benefits: Comprehensive benefits including eligibility for a company-sponsored 401(k), pension plans, vacation benefits, medical/dental/vision and prescription drug plans, flexible spending accounts, life insurance and death benefits, various leave benefits, and well-being programs (employee assistance, fitness benefits, and employee clubs and activities).