Computational Biologist II (Protein Engineering)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 SummaryWe 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.ResponsibilitiesProtein Engineering / Protein Modeling (Primary Focus)Protein–protein and protein–ligand interaction modelingDe novo enzyme, scaffold, and binder designStructure prediction, refinement, and conformational analysisMolecular dynamics simulations and structure based optimizationIntegration of AI/ML tools for protein design and optimizationDevelopment and maintenance of reproducible computational protein engineering workflowsClose collaboration with wet lab scientists to guide experimental design, interpretation, and iterationGeneral ResponsibilitiesDesign, plan, and lead computational tasks for small multidisciplinary project teamsProvide technical leadership and mentoring within protein engineering effortsPresent results and technical updates to internal teams, collaborators, and external sponsorsContribute to and/or lead development of scientific publications, conference presentations, and proposalsIdentify new technical opportunities and contribute to the growth of protein engineering and computational biology capabilitiesSupport administrative and project management tasks that ensure timely and high quality project deliveryKey QualificationsBachelor'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 QualificationsPh.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 fieldDeep expertise in computational protein engineering, including AI/ML enabled protein design, structural modeling, or optimizationExtensive expertise using protein design tools (e.g.
RFdiffusion, ProteinMPNN, AlphaFold, Rosetta based workflows, etc.) for protein-binder and enzyme designDemonstrated ability to reproducibly script and code using Python and/or Bash/Unix shellExperience 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 toolsExperience 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 characterizationProven ability to work effectively in multidisciplinary team environmentsAbility to independently troubleshoot technical challenges and rapidly adopt new modeling tools or workflowsStrong written and oral communication skillsU.S. citizenship with the ability to obtain and maintain required security clearancesProtein-ligand interaction modeling de novo enzyme and binder design, molecular dynamics simulationsExperience integrating AI/ML tools for protein design (e.g., RFdiffusion3), structure prediction (e.g., AlphaFold3), and optimization (e.g., Rosetta) into computational workflowsExperience deploying computational workloads on HPC or cloud architectures