Research Scientist - Biomolecular Simulation & Dynamics

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 protein discovery, engineering and computational sciences, we are committed to delivering next wave of biomedicines.

As we advance into increasingly complex modalities (multi-specific antibodies, conjugations, fusions proteins), computational approaches relying on static structure is no longer sufficient. We’re seeking a simulation expert to strengthen physics-based computational approaches for Lilly biotherapeutics discovery.  This position is based at the Lilly Biotechnology Center in San Diego, at the intersection of Computational Science, AI / ML Platforms, Protein Bioscience, Automation, Protein Engineering, and Information Technology. This role offers a unique opportunity to build simulation capabilities with full organizational support, work on diverse therapeutic modalities across multiple disease areas, and shape how BioTDR approaches biologics design.

Specifically, the candidate will drive all-atom and coarse-grain molecular dynamics (MD) to deliver decision-ready insights on antibodies, multi-specifics, proteins, and conjugates, to understand mechanism of action (MOA) and to enable rational based designs. Additionally, the candidate will build an industry-leading, integrated computational pipeline to accelerate biotherapeutic discovery and delivery.

Primary Responsibilities :

Run MD to assess protein stability, binding interfaces / epitopes, conformational dynamics, glycan effects, and pH / ion impacts

Develop and deploy coarse-grained MD workflows (e.g., MARTINI 3) to rapidly triage self-association or aggregation risk, profile membrane interactions, and characterize domain-level dynamics.

Apply enhanced-sampling techniques to capture loop motions, macrocycle ring flips, and other rare conformational events; summarize with quantitative, decision-oriented metrics.

Partner with project teams to prioritize designs; reconcile predictions and calculations with experimental data.

Develop methods predicting MHCII-peptide registration

Build validated MD playbooks / SOPs (system prep, constant-pH / pKa workflows, force-field selection, QC / validation) with benchmarks on antibodies, multi-specifics, peptides or macrocycles.

Develop and apply free energy perturbation (FEP) or comparable computational methods to screen binding affinity and guide design choices.

Publish MD-derived features (e.g., RMSF, contact persistence, hydration / SASA patches, H-bond occupancies) to the ML platform with clear data contracts.

Provide conformational ensembles for docking rescoring and structural constraints for generative design and protein-LM-based optimization.

Basic Qualifications

PhD (or MS and 5+ years of experience) in Computational Biophysics, Chemistry, or related fields.

Additional Skills and Preferences

5+ years applying MD in drug / biotherapeutics discovery (industry or close industry-collab academic) preferred.

Hands-on with OpenMM / GROMACS / AMBER / NAMD and PLUMED; strong analysis skills (MDAnalysis / MDTraj / PyEMMA).

Demonstrated coarse-grain MD expertise (e.g., MARTINI 3) for aggregation / LLPS / self-association or membrane interactions.

Experience in modeling antibodies / biologics (glycosylation, developability liabilities) and / or peptides / macrocycles.

Competency with enhanced sampling, uncertainty quantification, and delivering clear, decision-grade communication.

Proficiency in Python for system preparation, workflow automation, and data analysis; comfortable with Linux / HPC environments.

Experience with physics-based free-energy methods (FEP / TI), constant-pH MD and pKa prediction pipelines.

Familiarity with statistical modeling / ML (e.g., feature engineering, simple baselines) and integrating simulation outputs into predictive models.

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 environment.

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 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

$138,000 - $224,400

Full-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.

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