Advances in Computational Protein Engineering

October 17, 2017

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Time: 5:00 PM - 7:00 PM
Location: Lobby

Join Cyrus Biotechnology for a panel that will illustrate recent advances in computational protein engineering. Computationally designed therapeutic proteins are in the clinic, and computationally optimized enzymes are producing ingredients of value sustainably and cost effectively. Can your organization leverage these technologies? You won't know until you learn more. 



  • 5:00pm - 5:45pm: Registration, Refreshments and Networking
  • 5:45pm - 7:00pm: Panel Presentations and Discussion


  • Lucas Nivon, CEO of Cyrus Biotechnology

Dr. Nivon will present an overview of published and experimentally verified advances in computational protein engineering, and will demonstrate some modeling workflows with sample software based on the Rosetta protein modeling toolkit first developed at Professor David Baker’s laboratory at the University of Washington. Following Dr. Nivon’s overview, four panelists will present various examples of protein modeling.

  • Jason Donald, Director of Protein Engineering, Manus Biosynthesis

Dr. Donald will describe ways in which computational protein engineering can be used to design novel enzymes for applications in metabolic engineering and synthetic biology. Manus Bio recreates plant biosynthetic pathways in microorganisms to produce natural ingredients economically and sustainably through fermentation. Computational protein engineering improves the enzyme design process for these pathways and allows optimization across a number of important parameters, including solubility, stability, specificity, and catalytic efficiency. These tools can be leveraged for both rational mutagenesis as well as the design of more extensive semi-combinatorial enzyme libraries for screening.

  • Elisabeth Narayanan, Computational Scientist, Valera, a Moderna Therapeutics Venture

Dr. Narayanan began her career in computational protein design in Tanja Kortemme’s lab at UCSF, developing Rosetta based methodologies for protein interface design, flexible backbone prediction of mutational tolerance, and multi-state design. Since then, she has used a variety of protein engineering tools in an industry setting at Moderna to advance the discovery of mRNA based vaccines and therapeutics.

  • Seth Cooper, Assistant Professor, College of Computer and Information Science, Northeastern University
  • Firas Khatib, Assistant Professor, Computer and Information Science, UMass Dartmouth

Rather than solving problems with a purely computational approach, combining humans and computers can provide a means for solving problems neither could solve alone. As a primary example, we will discuss Foldit, an online citizen science game about computational protein structure prediction and design. Foldit players have contributed to several scientific discoveries through gameplay. Independent of the Foldit game, Foldit Standalone allows the Foldit protein manipulation interface to be used on locally imported structures. Foldit Standalone has successfully been used by scientists to create and experimentally test an enzyme to break down gluten, potentially leading to a treatment of gluten intolerance and celiac disease.