Biotech startups join AWS and other partners in open source project to help design new proteins – GeekWire

Experimentally determined structure of a bacterial protein, compared to structures produced by AlphaFold2 and OpenFold. (OpenFold Image)

Three Seattle biotech companies are joining forces to support the development of open source protein design and folding software.

The project, called OpenFold, brings together Cyrus Biotechnology, Outpace Bio and Arzeda, startups developing new proteins that can be used as drugs or in industrial applications.

“It doesn’t make sense for all of us to duplicate the same work,” Cyrus CEO Lucas Nivon told GeekWire. “Especially if it doesn’t give any company a competitive advantage.”

The three companies are joined by Prescient Design, an accelerator within Genentech, and the lab of Mohammed AlQuraishi, assistant professor of systems biology at Columbia University. The project is supported by Amazon Web Services for free, and other companies and organizations are considering joining, Nivon said.

The consortium improves AlphaFold, a machine learning tool developed by Alphabet’s DeepMind that predicts how proteins fold into three-dimensional shapes.

Protein is the building blocks of the body and the basis of many treatments. Exploitation of this software promises to accelerate the development of new drugs, enzymes and biomaterials.

DeepMind released a public version of its tool last July, and since then several groups have improved it. AlQuraishi and his team recently released a version, called OpenFold, that incorporates updated formation datasets of known three-dimensional protein structures. OpenFold even slightly outperforms DeepMind’s most recent open version of AlphaFold, AlQuraishi said. in a tweet.

It’s now easy to update OpenFold with new data, add different kinds of features, and fine-tune the tool. Specific areas of interest could include antibody design, small molecule prediction, and understanding protein movement and alternative conformations.

Nivon likens the new consortium to Linux, an open-source project that enables new software to be built. He anticipates that some of the new tools will be open source and other proprietary.

The focus is on AlphaFold, not a similar tool built by the University of Washington’s Institute for Protein Design, which created Cyrus, Outpace, and Arzeda.

“So far, the accuracy we’re seeing with AlphaFold so far is unmatched,” Nivon said. His team, however, relies on other software from IPD for their designs. And the release of IPD’s tool prompted DeepMind to release a public version at the same time.

Both tools stunned the scientific community with their speed and accuracy in predicting protein shapes, and won Science magazine’s prestigious Breakthrough of the Year award last winter.

DeepMind is not a member of the consortium but created Isomorphic Labs, a startup to leverage its software for drug discovery.

OpenFold is a project of the nonprofit Open Molecular Software Foundation and is supported by Amazon through its AWS Open Data Sponsorship Program, which also hosts OpenFreeEnergy and Open Forcefield to support drug design efforts.


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