Computational Protein Structure Prediction Jobs

Battelle delivers when others can't. We conduct research and development, manage national laboratories, design and manufacture products and deliver critical services for our clients-whether they are a multi-national corporation, a small start-up or a government agency.
We recognize and appreciate the value and contributions of individuals from a wide range of backgrounds and experiences and welcome all qualified individuals to apply.
Job Summary
We are seeking a Computational Biologist II with deep expertise in protein modeling and engineering. This requisition is focused on candidates who excel at computational protein design, who want to be part of a team focused on optimizing and testing protein structure-function relationships to solve real-world problems, and who thrive in fast moving, multidisciplinary R&D environments. Our team values creativity, rapid learning, and collaborative problem solving.
As a Computational Biologist II (Protein Engineering), you will contribute to cutting edge research by applying computational approaches to protein structure prediction, design, and optimization. You will provide technical leadership on challenging internally and externally funded R&D programs and collaborate closely with experimental biologists, chemists, and engineers.
The ideal candidate is a self directed scientist who is comfortable building new computational workflows, integrating AI/ML enabled modeling tools, and translating biological hypotheses into deployable design strategies. Proficiency in Python (and/or related scientific programming languages) and experience with modern protein modeling and design frameworks (e.g., AlphaFold3, ProteinMPNN, RFdiffusion, Rosetta) are highly desirable. The candidate should be a team player who can work collaboratively with experimental scientists who will implement and test designs.
Responsibilities
Protein Engineering / Protein Modeling (Primary Focus)
You will be expected to demonstrate deep expertise in one or more of the following areas:

• Protein-protein and protein-ligand interaction modeling
• De novo enzyme, scaffold, and binder design
• Structure prediction, refinement, and conformational analysis
• Molecular dynamics simulations and structure based optimization
• Integration of AI/ML tools for protein design and optimization
• Development and maintenance of reproducible computational protein engineering workflows
• Close collaboration with wet lab scientists to guide experimental design, interpretation, and iteration

General Responsibilities

• Design, plan, and lead computational tasks for small multidisciplinary project teams
• Provide technical leadership and mentoring within protein engineering efforts
• Present results and technical updates to internal teams, collaborators, and external sponsors
• Contribute to and/or lead development of scientific publications, conference presentations, and proposals
• Identify new technical opportunities and contribute to the growth of protein engineering and computational biology capabilities
• Support administrative and project management tasks that ensure timely and high quality project delivery

Key Qualifications

• Bachelor's degree in related field with 2 years of experience or master's degree in related field; or an equivalent combination of education and or experience in a related field.

Preferred Qualifications

• Ph.D.; or M.S. plus 5 years of experience; or B.S. plus 10 years of experience in biochemistry, biophysics, computational biology, structural biology, or a closely related field
• Deep expertise in computational protein engineering, including AI/ML enabled protein design, structural modeling, or optimization
• Extensive expertise using protein design tools (e.g. RFdiffusion, ProteinMPNN, AlphaFold, Rosetta based workflows, etc.) for protein-binder and enzyme design
• Demonstrated ability to reproducibly script and code using Python and/or Bash/Unix shell
• Experience with scientific computing and data analysis libraries (e.g., NumPy, pandas, SciPy, PyTorch/JAX, matplotlib)
• Hands on experience installing, maintaining, and operating open source protein modeling and simulation tools
• Experience with containerized software environments (e.g., Conda, Docker, Apptainer/ Singularity)
• Strong fundamental understanding of protein biochemistry and common laboratory procedures relevant to protein expression, purification, and characterization
• Proven ability to work effectively in multidisciplinary team environments
• Ability to independently troubleshoot technical challenges and rapidly adopt new modeling tools or workflows
• Strong written and oral communication skills
• U.S. citizenship with the ability to obtain and maintain required security clearances
• Protein-ligand interaction modeling de novo enzyme and binder design, molecular dynamics simulations
• Experience integrating AI/ML tools for protein design (e.g., RFdiffusion3), structure prediction (e.g., AlphaFold3), and optimization (e.g., Rosetta) into computational workflows
• Experience deploying computational workloads on HPC or cloud architectures

Benefits: Live an Extraordinary Life
We care about your well-being, not just on the job. Battelle offers comprehensive and competitive benefits to help you live your best life.

• Balance life through a compressed work schedule: Most of our team follows a flexible, compressed work schedule that allows for every other Friday off-giving you a dedicated day to accomplish things in your personal life without using vacation time.
• Enjoy enhanced work flexibility, including a hybrid arrangement: You have options for where and when you work. Our Together with Flexibility model allows you to work 60% in-office and 40% remote, with Monday and Tuesday as common in-office days, dependent on team and position needs.
• Take time to recharge: You get paid time off to support work-life balance and keep motivated.
• Prioritize wellness: Stay healthy with medical, dental, and vision coverage with wellness incentives and benefits plus a variety of optional supplemental benefits.
• Better together: Coverage for partners, gender-affirming care and health support, and family formation support.
• Build your financial future: Build financial stability with an industry-leading 401(k) retirement savings plan. For most employees, we put in 5 percent whether you contribute or not, and match your contributions on top of that.
• Advance your education: Tuition assistance is available to pursue higher education.

A Work Environment Where You Succeed
For brilliant minds in science, technology, engineering and business operations, Battelle is the place to do the greatest good by solving humanity's most pressing challenges and creating a safer, healthier and more secure world.
You will have the opportunity to thrive in a culture that inspires you to:

• Apply your talent to challenging and meaningful projects
• Receive select funding to pursue ideas in scientific and technological discovery
• Partner with world-class experts in a collaborative environment
• Nurture and develop the next generation of scientific leaders
• Give back to and improve our communities

Vaccinations & Safety Protocols
Battelle may require employees, based on job duties, work location, and/or its clients' requirements to follow certain safety protocols and to be vaccinated against a variety of viruses, bacteria, and diseases as a condition of employment and continued employment and to provide documentation that they are fully vaccinated. If applicable, Battelle will provide reasonable accommodations based on a qualified disability or medical condition through the Americans with Disabilities Act or the Rehabilitation Act or for a sincerely held religious belief under Title VII of the Civil Rights Act of 1964 (and related state laws).
Battelle is an equal opportunity employer. We provide employment and opportunities for advancement, compensation, training, and growth according to individual merit, without regard to race, color, religion, sex (including pregnancy), national origin, sexual orientation, gender identity or expression, marital status, age, genetic information, disability, veteran-status veteran or military status, or any other characteristic protected under applicable Federal, state, or local law. Our goal is for each staff member to have the opportunity to grow to the limits of their abilities and to achieve personal and organizational objectives. We will support positive programs for equal treatment of all staff and full utilization of all qualified employees at all levels within Battelle.
The above statements are intended to describe the nature and level of work being performed by people assigned to this job. They are not intended to be an exhaustive list of all responsibilities, activities and skills required of staff members. No statement herein is intended to imply any authorities to commit Battelle unless special written permission is granted by Battelle's Legal Department.
For more information about our other openings, please visit www.battelle.org/careers