The Impact of the IPD

Founded by Dr. David Baker in 2012, the mission of the Institute for Protein Design (IPD) is to design a new world of proteins that address 21st-century challenges in medicine, energy, and technology. See Map 1 below for the home town locations of current IPD scientists, and staff who have come from around the world to learn protein design and its applications at the IPD.

Since 2014, the IPD has spun out five new biotechnology companies and collectively raised over $61 million in financing. These include:

  • Arzeda: protein design for synthetic biological production of valuable chemicals
  • Cyrus Biotechnology: Rosetta software as a cloud computing service for the biopharmaceutical industry
  • PvP Biologics: a gluten-busting enzyme for celiac disease
  • Virvio: designed proteins to block the flu virus
  • Icosavax: a new vaccine for respiratory syncytial virus (RSV), a deadly virus affecting newborns and the elderly

Over several years, the Baker lab and numerous former postdoctoral fellows and graduate students of the Baker lab (See Map 2 of Former Baker Lab members now faculty at other institutions) have collectively worked to generate a computer program called Rosetta to model the folds and test theories on why a given amino acid sequence led to a specific design.

Rosetta is based on Anfinsen’s thermodynamic hypothesis of protein folding: the folded state of a protein is the lowest energy state accessible to the polypeptide chain. The protein structure prediction problem then is to identify, for a given amino acid sequence, the lowest energy structure. The protein design problem is to identify, for a desired structure or function, an amino acid sequence whose lowest energy state is that structure (or has the desired function). To carry out these prediction and design calculations, we have been developing a computer program called Rosetta which is widely distributed now through the Rosetta Commons.

We enlisted volunteer citizen-scientists by developing Rosetta@Home, which allows anyone with a computer or cell phone to support our research. Our Rosetta software is now running calculations on nearly a billion computing devices worldwide, requiring ~10% of the UW’s internet bandwidth. Soon after we started the Rosetta@home project, contributors watching video representations of origami-like protein folding calculations became curious themselves and wanted to see if they could help solve protein challenges. So we created Foldit, a multiplayer online game where thousands of volunteers compete to solve new protein folding puzzles — everything from the structure of AIDS proteins to designs for food poisoning cures. See below the growth Foldit player activity over the years.

Map 1: Home town locations of current IPD scientists

Home town locations of all scientific researchers, and staff of current IPD affiliate labs (Baker, King, DiMaio, Gu, Bradley, and IPD Core Labs)

Map 2: Former Baker Lab members now faculty at other institutions

Former Baker lab postdocs or graduate students who are now faculty at other institutions world wide.

FoldIt: Growth and player activity