Director / Sr. Director - Computational Peptide Design

Company: Initial Therapeutics, Inc.
Location: San Diego
Posted on: June 1, 2025

Job Description:

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.Lilly's Biotechnology Discovery Research (BioTDR) organization has a track record for delivering novel biotherapeutic medicines advanced into clinical research in key areas of unmet medical needs, across a variety of therapeutic areas. Integrating biology with innovative scientific capabilities in peptide discovery, engineering and computational science, we are committed to delivering next wave of peptide therapeutics.We are seeking an exceptional, senior-level computational peptide scientist to create novel technology accelerating peptide discovery and design. This position lies at the cross-section of computational science, peptide discovery and engineering, automation, and Information technology, is located at the Lilly Biotechnology Center in San Diego. The successful candidate will lead a small team and spearhead the development of complex workflow and pipelines to enable the selection, design, and optimization of peptide modalities. Working in this collaborative environment with access to cutting-edge technologies and resources, you have the opportunity to contribute to groundbreaking peptide therapies. If you are passionate about advancing peptide drug discovery through computational innovation, we encourage you to apply for this exciting leadership role.Primary Responsibilities:

• Strategize and lead the design of bespoke peptide libraries (target specific or property controlled), using advanced computational techniques, including bio-/chem-informatics and AI/ML
• Develop and implement informatics tools for NGS data visualization and processing to enable peptide hit selection
• Drive the creation of new computational methods to enablepeptide SAR, improving activity, selectivity, stability and permeability.
• Lead the development and implementation of advanced computational methods (sequence-based, physics-based) for target, and peptide modeling and optimization, leveraging AI/ML to improve predictive modeling and candidate selection
• Work closely with peptide group, collaborate with multidisciplinary teams to integrate computational strategies in peptide hit discovery and hit to lead optimization
• Oversee codebase and model management to support reproducibility and collaboration
• Stay current with the latest advancements in AI/ML and drive transformation of methods for impactful applications
• Present scientific findings and strategies to both internal and external stakeholdersBasic Qualifications
  • Ph.D. in Computational Chemistry, Biology, chemistry, physics or a related field
  • Minimum of 5 years of relevant experience beyond education/postdoctoral training, in industry or research organization (10+ years desired)Additional Skills and Preferences
    • Strong expertise in NGS bioinformatics and computational peptide design
    • Experience related to application of cheminformatics in peptide library design Experience with non-canonical amino acids and their integration into peptide design
    • Proficiency in sequence-based and physics-based computational methods, including MOE, Schrodinger LiveDesign, Rossetta, other visualization and analysis software
    • Proficiency in general molecular modeling techniques (docking, molecular simulation, homology modeling, quantum mechanics, ligand- and structure-based design)
    • Advanced knowledge and hands-on experience of ML/AI applications in peptide space
    • Proficiency in programming languages (such as Python) to curate and analyze data at scale and to implement new metrics to predict and select peptide designs
    • Proven track record of leading successful computational peptide discovery or design projects in the pharmaceutical, biotechnology, or research organization
    • Experience in managing and developing teams of computational scientists
    • Experience with cloud computing platforms and high-performance computing environments
    • Excellent communication and presentation skills, with the ability to convey complex technical concepts to diverse audiences
    • Ability to work productively and collaboratively in an interdisciplinary team environmentAdditional Information--- Location: San Diego, CALilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form () for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, 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 are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women's Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.Actual compensation will depend on a candidate's education, experience, skills, and geographic location. The anticipated wage for this position is$184,500 - $321,200Full-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.#WeAreLilly
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Keywords: Initial Therapeutics, Inc., Aliso Viejo , Director / Sr. Director - Computational Peptide Design, Executive , San Diego, California