Computational Biologist

Battelle Memorial Institute; Kentucky; On-site; USD 90,000 - 130,000; Full time

Job summary

Battelle Memorial Institute in Kentucky is seeking a Computational Biologist II with deep expertise in protein modeling and engineering to advance design, testing, and optimization of protein structure-function relationships on fast-moving R&D programs.

You will contribute to cutting-edge computational work, lead tasks for multidisciplinary teams, and collaborate with wet labs to guide experiments and interpretation, leveraging AlphaFold, RFdiffusion, ProteinMPNN, Rosetta, and related tools.

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 experience.
• Strong expertise in computational protein engineering, including AI/ML enabled design, modeling, or optimization.
• Experience with open-source protein modeling tools and scripting in Python/Bash.

Responsibilities

• Design, plan, and lead computational tasks for small multidisciplinary project teams.
• Provide technical leadership and mentoring within protein engineering efforts.
• Present results to internal teams, collaborators, and external sponsors.
• Contribute to scientific publications, conference presentations, and proposals.
• Identify new technical opportunities and support growth of protein engineering capabilities.
• Support administrative and project management tasks for timely delivery.

Skills

Python

AI/ML

Protein design

Rosetta

AlphaFold

RFdiffusion

PyTorch/JAX

NumPy

Pandas

Team leadership

Communication

Education

Ph.D.

M.S. + 5 years experience

B.S. + 10 years experience

Tools

RFdiffusion

ProteinMPNN

AlphaFold

Rosetta

Conda

Docker

Apptainer/Singularity

Job description

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)

• 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 pred