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Sr. Scientist, Computational Protein Design







Job Description

Bluestem Biosciences, Inc., is designing biology with the end in mind, to enable existing infrastructure in the Midwest for industrial biotechnology.
We are leveraging digital biology to facilitate discovery for biomanufacturing, focused on the sustainable production of chemicals and materials.

We are seeking a full-time Scientist in Computational Protein Design to join Bluestem’s top-talented scientific team. Ideal candidates will be well versed in deep learning techniques for protein design and applying those techniques to solve the hardest challenges in industrial protein design. Additionally, ideal candidates extend beyond the mastery of existing tools and methods,  with intuition about gaps in the current approaches and a desire  to fundamentally change existing paradigms. This role will lead  efforts in curating and best-in-class tools and building new functionalities that will fit into a mosaic of multi-disciplined computational tools and workflows that drive Bluestem’s scientific endeavors in synthetic biology.  


  • Curate available tools and develop a strategy for the incorporation of those tools into an in-silico experimental and TEA platform
  • Develop deep learning methods for enzyme and protein design
  • Participate in the implementation and architecture of protein design related tools into the Bluestem computational platform
  • Continually refine and optimize strategy for structure-based and reaction-based predictive tools to enhance accuracy and effectiveness of the computational tools
  • Stay up-to-date with cutting edge computational biology, in particular structure-based, biocatalyst AI/ML tools
  • Work to automate in silico workflows, data ingestion and analysis.
  • Ph.D. in Computational Biology, Computer Science, or related field  with 3+ years of industry  or academic (post-doc) experience
  • A strong understanding of protein biophysics and structure
  • Extensive knowledge of relevant programming languages and available computational tools
  • Working knowledge wet-lab techniques and workflows in protein expression and characterization
  • Strong communication skills, both written and verbal and ability to work in a dynamic and fast-paced environment (start-up!)
  • Self-starter and ability to lead projects, build relationships and be a vocal representative of the company
  • Working knowledge of available computational tools, capabilities and strategies
  • Organizational agility and the ability to show collaboration and interest across the organization to bring together multi-disciplines and synthesize for external communications
  • Possess a Growth Mindset and open mind that seeks continuous learning from feedback, setbacks and failure on the journey to achieving results
  • Embraces diversity,  models equity in action  and contributes to a high trust and  inclusive  work environment that supports team members in doing the best work of their careers at Bluestem
  • Humble, Hungry and Smart with a grounded “otherish” approach to collaboration, an ownership mentality with a bias towards execution, and the ability to read and lead yourself so that you can more effectively read and lead others

Bluestem is excited to offer a remote-first working model. Team members can work primarily remotely. Conditions permitting, teams will meet in person every quarter or two at Bluestem’s hub, in Omaha, NE. We believe this balanced, flexible approach gives our team members the best of both worlds: plenty of focus time along with in-person collaboration that fosters trust, unlocks creativity, and further fuels innovation.

Bluestem is proud to be an equal opportunity workplace. We are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. We also consider qualified applicants regardless of criminal histories, consistent with legal requirements.

If you have a disability or special need that requires accommodation, please let us know by emailing

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