Advisor of Computational Peptide Biochemistry

Job ID: R-107641Company: LillyLocation: Pasadena, California, United States of AmericaJob Type: Full TimeCategory: Research & DevelopmentPosted Date: 2026-07-14At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us. Organization Overview:At Lilly, we serve an extraordinary purpose. For 150 years, we have worked tirelessly to discover medicines that make life better. These discoveries start in Lilly Research Laboratories, where our scientists work to create new medicines that will help solve our world’s greatest health challenges. Protomer team at Lilly focuses on chemical biology, molecular switches and oral macrocyclic peptide platforms. This position is for a senior computational biologist-biochemist with extensive background and knowledge in the field.We are seeking an Advisor/Senior Advisor in Computational Peptide Chemistry to drive peptide discovery programs by providing computational modelling support for the team, and building computational and AI/ML-based infrastructure at Protomer Team in Eli Lilly. Modeling and computational support will be for multiple projects including support for oral macrocycle efforts.The successful candidate will work closely with peptide discovery team, structural biologists, assay biologists and medicinal chemists to guide peptide structure-activity relationship studies from hit identification to lead optimization. The ideal candidate will combine deep technical computational expertise with practical peptide discovery and medicinal chemistry knowledge provided by other members of peptide discovery team to accelerate lead time of peptide discovery programs. Ideal candidate is a creative computational scientist for the integration of the latest computational and AI/ML-based approaches into the automated and high-throughput peptide drug discovery workflows.The ideal candidate is a significant contributor and leading a highly integrated, agile, and collaborative team effort and expected to manage the scientific portfolio, the business supporting the portfolio, and mentoring of junior scientists within the oral macrocycles group at Protomer. Ideal candidate is expected to have demonstrated success in similar roles with proven track record of leading both scientific rationale, planning and execution leading to success in making medicines. This individual will also be expected to be able to independently lead projects, help shape the team and strategy of the group, contribute significantly to prioritization of the team objectives and interact with and create and nurture the cross-functional relationships interacting with various therapeutic areas such diabetes and obesity, neuroscience, immunology and oncology.Responsibilities:Contribute as the lead biochemist and assay biologist for the team on macrocyclic discovery, contributing both insight and developing strategy for assays for various efforts in the groupWork on (both directionally and operationally) molecule testing efforts from lead identification to lead optimization and contribute along the way to phase 1b and beyond Provide assay development expertise, and support for macrocyclic peptide discovery projectsProvide biological insight based on detailed biology of various targets to better focus molecule discovering efforts that are informed based on the biology of the targetsDevelop methodologies, protocols and run SPR and other protein binding assays for characterization of compoundsCharacterize complete functionality of protein reagents, provide both insight and oversight into quality and tracking of protein reagents, be able to independently lead a small team of biochemists and biologists to support a large molecule discovery group with various targets and assets at different stages of discoveryLearn about and enhance the platform technology efforts at Protomer to accelerate assays and biochemical workflows including automationWork collaboratively in the group to achieve a common goal but also provide independent perspective and scientific rationale and contribute to strategy and execution. Take on dedicated efforts towards targets of high conviction and utilize speed and prioritization to advance assay efforts both at Protomer and wider Lilly groups and through collaboration with the rest of research organization Inspire people to collaborate in inventing great medicines by removing barriers, committing to high quality scientific hypotheses, and accelerating where possible. Keep safety as a top priority at all times, striving toward a proactive safety culture. Be a good team player and work effectively, responsibly and professionally with colleagues at Protomer and across Lilly. Minimum Qualifications:PhD in computational chemistry, medicinal chemistry, computational biology, machine learning, cheminformatics, biophysics, or closely related discipline0-3 years of drug discovery experience with demonstrated track record of computational impact on peptide discovery programs in academia, biotech, or pharmaStrong track record in AI/ML, computational tools and molecular designs for linear and cyclic peptides and proactively apply new approaches to develop peptide drug design toolsPreferred Qualifications:Experience integrating generative AI and/or LLM, structure-based design, free energy perturbation to peptide SAR studies from hit identification to lead optimization in peptide drug discovery programsProficiency across computational tools in molecular docking, molecular dynamics simulation, FEP/free-energy methods, QSAR/ADMET modellingExperience with virtual screening campaigns, structure-based peptide drug design and ability to interpret crystallography or cryo-EM data into implement in the drug design tools computational design strategiesStrong programming, preferably Python, with experience using cheminformatics toolkits such as RDKit and modern data science workflowsFamiliar with cloud-based or high-performance computing environmentsFamiliar with peptide screening technologies (mRNA display, one-bead-one-compound libraries, yeast display, phage display, etc) to accelerate design-make-test-analyse cycle of peptide discovery programsFamiliar with peptide medicinal chemistry principles, physicochemical property optimization of peptide as modalities, oral macrocyclic peptide properties, ADME/PK conceptsPartner closely with peptide discovery scientists, peptide chemists and medicinal chemists to translate computational data into hit identification/lead optimization strategies Additional Information:Some domestic and international travel is anticipated and expected. Lilly 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 (AMECA), Black Employees at Lilly (View email address on click.appcast.io), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is$166,500 - $266,200Full-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.#WeAreLillySkillscomputational modelingpeptide discoveryai/ml integrationmolecular dockingmolecular dynamics simulationfep/free-energy methodsqsar/admet modellingvirtual screeningstructure-based designprotein binding assaysprotein reagent characterizationpythonpeptide medicinal chemistryrdkitdata science workflowscloud-based computinghigh-performance computingadme/pk conceptsstakeholder managementmentoring