The UW Medicine Institute for Protein Design (IPD) today released a new open-source model for creating proteins with specific functions, called RFD4-Proteina. It is the first AI protein model the University of Washington has co-developed with semiconductor giant Nvidia.
The release comes on the heels of a major computing boost. Earlier this month, IPD announced it had received a large grant of computing power from Nvidia CEO Jensen Huang and his wife, Lori Huang, through their foundation. In June, the institute began accessing Nvidia graphics processing units, or GPUs, through cloud company CoreWeave. The grant is expected to support the institute for a year.
“RFD4-Proteina will open the door to new solutions in medicine, sustainability, materials and biotechnology,” David Baker, director of IPD and a 2024 Nobel laureate in chemistry, said in a statement. He earlier told GeekWire that the foundation’s grant has been “transformational” for the institute’s work.
IPD has used deep learning to develop and release a series of tools, including RoseTTAFold for predicting protein structures and RFdiffusion (RFD) for designing new proteins. The new model’s name nods to RFD and references Nvidia’s Proteina-Complexa computational models.
The team is touting RFD4-Proteina as “a considerable improvement over previous methods” that is faster and requires significantly less computational power.
The models have allowed researchers to design proteins never imagined before, with potential as drugs for challenging diseases or as tools for managing environmental waste such as toxic chemicals and plastics, among other applications. The IPD lists 11 spinout companies, including vaccine developer Icosavax and protein-design startup Archon Biosciences.
Seth Woodbury used RFD4-Proteina in his enzyme work as a , a UW bioengineering predoctoral candidate. “In just a few days we designed a pesticide-degrading enzyme that performs many fold better than my previous best, which took months to design,” he said. Woodbury last year published a paper in Nature on enzyme research.
At IPD, the RFD4-Proteina work was led by UW doctoral students Nathaniel Corley, Maxwell Kazman and Rafi Brent, along with Kieran Didi, a visiting student from the University of Oxford.
RFD4-Proteina is available through Berkeley Software Distribution.