Post-doctoral Computational Chemist, Advanced Molecular Design

BioSpace; Indianapolis (IN); On-site; USD 58,000 - 123,000; Full time

Benefits offered by this job

401(k) plan with company match

Health, dental, vision insurance

Vacation benefits and wellness program

Job summary

Lilly in Indianapolis, Indiana is seeking a Post-doctoral Computational Chemist to join the Advanced Molecular Design (AMD) team within Lilly Research Labs. You will apply quantum mechanics, MD simulations, and AI/ML approaches to accelerate drug discovery, collaborating with chemists and biologists to advance molecules from hits to candidates.

You will build workflows, maintain computational infrastructure, and communicate findings through presentations, with a fixed-term appointment up to two

Qualifications

• Ph.D. in Computational Chemistry or related field completed by Aug 2026.
• Authorized to work in the United States full-time; visa sponsorship not provided.

Responsibilities

• Perform quantum mechanical calculations, MD simulations, and free energy calculations for structure-based drug design.
• Develop infrastructure for quantum mechanics, MD, and free energy methods across projects.
• Automate workflows across computational tools for throughput and reproducibility.
• Gain deep knowledge of Schrödinger, MOE, Gaussian/Orca/GAMESS, and MD packages (OpenMM, AMBER, CHARMM, GROMACS, Desmond).
• Stay current with AI/ML methods for molecular property prediction and design.
• Collaborate with medicinal chemists, structural biologists, and toxicologists to advance portfolio molecules.
• Present progress at internal and external meetings; maintain timelines.
• Support discovery scientists to advance leads to quality drug candidates.

Skills

Python scripting

Team collaboration

Problem solving

Communication

HPC experience

Education

Ph.D. in Computational Chemistry or related field

Tools

Schrödinger

MOE

Gaussian

Orca

GAMESS

OpenMM

AMBER

CHARMM

GROMACS

Desmond

RDKit

OpenEye

MDAnalysis

NumPy

SciPy

pandas

GitHub

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.

Post-doctoral Computational Chemist

Location: Indianapolis, Indiana, United States of America

Organization Overview

At Lilly, we serve an extraordinary purpose. For 150 years, we have worked diligently 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. We are looking for a highly motivated Postdoctoral Computational Chemist to join our Advanced Molecular Design (AMD) team within Lilly Research Labs, Indianapolis, Indiana.

AMD applies cutting-edge computational methods to accelerate drug discovery across Lilly's portfolio. Our team integrates structure-based design, quantum mechanics, molecular dynamics, free energy calculations, and AI/ML approaches to accelerate and advance molecules from hit identification through clinical candidate selection.

Responsibilities

• Execute advanced quantum mechanical calculations, molecular dynamics simulations and free energy calculations to study protein motion, protein-ligand interactions, and protein-protein interactions in support of structure-based drug design.
• Build and maintain informatic infrastructure enabling broad utilization of quantum mechanics, molecular dynamics, and free energy methods across drug discovery projects.
• Script and automate workflows across computational software platforms to maximize throughput and reproducibility of molecular calculations.
• Develop deep working knowledge of computational chemistry suites including Schrödinger, MOE, Gaussian/Orca/GAMESS, and one or more MD packages (OpenMM, AMBER, CHARMM, GROMACS, or Desmond).
• Stay current with emerging methods in computational drug discovery, including AI and machine learning models for molecular property prediction and design.
• Work as part of a multidisciplinary team—including medicinal chemists, structural biologists, biologists, statisticians, and toxicologists—to deliver computational insights that advance drug discovery projects.
• Maintain critical timelines and communicate progress clearly through oral and written presentations at internal and external team meetings.
• Collaborate with discovery scientists to advance portfolio molecules from leads to quality drug candidates.

Basic Requirements

• Ph.D. in Computational Chemistry, Computer Science, Cheminformatics, Bioinformatics, Biophysics or a related field

with all completed requirements by August 2026

• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1

Additional Skills/Preferences

• Strong foundation in theoretical physical chemistry and organic chemistry
• Experience with molecular dynamics simulations, quantum mechanical or free energy calculation methods applied to protein-ligand systems
• Proficiency in Python and other scripting and programming languages
• Ability to work effectively both independently and in a collaborative team environment
• Knowledge of lead optimization using structure-based design and AI/ML models
• Familiarity with ADME and toxicology concepts in the context of drug discovery
• Experience working on HPC environment
• Experience with cheminformatics toolkits (RDKit, OpenEye) or structural analysis platforms (Schrodinger, ChemAxon)
• Proficiency in scientific computing libraries and APIs (MDAnalysis, NumPy, SciPy, pandas) beyond basic scripting
• Ability to build and automate computational workflows with minimal supervision
• Demonstrated experience with reproducible code practices and version control (GitHub/GitLab)
• Experience integrating structural biology data (cryo-EM, X-ray crystallography, NMR or AI-predicted structures) into computational design workflows
• Strong interpersonal, organizational, and problem-solving skills

Additional Information

• This is an onsite position based in Indianapolis, Indiana
• This position is not permanent. It is a fixed-term position up to 2 years with a possible 2 year extention.

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 (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance.

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

$58,000 - $123,200

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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