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Cyrus Biotech raises $8M for protein toolkit

Cyrus Bench on laptop
Cyrus Bench is a software platform for protein engineering. (Cyrus Biotech Photo)

Cyrus Biotechnology is getting an $8 million infusion for its cloud-based protein modeling and design toolkit, thanks to a Series A financing round.

The investment round was led by Trinity Ventures, with participation from OrbiMed AdvisorsSpringRock Ventures, the W Fund and individual investors, the Seattle-based venture said today in a news release.

Cyrus Biotech’s primary product, Cyrus Bench, is a software package based on Rosetta, a protein-modeling platform that was created at the University of Washington. Rosetta lets researchers twist and turn virtual models of protein molecules to create novel configurations. (It’s even spawned a video game for citizen scientists called Foldit and a screensaver called Rosetta@Home.)

Protein-folding has been compared to solving puzzles, or building molecular-scale keys for cellular locks. A protein molecule with the right shape could block a virus from invading a cell, or unlock a therapy for disease.

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Big data helps scientists solve protein puzzles

Protein models
The molecular diagram at left is a representation of a protein molecule known as DMT superfamily transporter YddG, generated by Rosetta@Home software. The diagram at right is a representation of the molecule as determined by experiments. (Sergei Ovchinnikov et al. / UW via AAAS / Science)

Molecular biologists have enlisted cutting-edge trends in genomics and big data to get a grip on one of the grand challenges of biotech: figuring out how protein molecules fold.

But they couldn’t have done it without the help of tens of thousands of volunteers.

The fruits of all that crowdsourced computer labor went public today in the journal Science. Researchers from the University of Washington and other institutions say they’ve solved more than 600 protein-folding mysteries – which represents a fair proportion of the estimated 5,200 protein families whose molecular structure was unknown.

Still more solutions are in the works, and solving those puzzles could lead to new types of medicines and synthetic molecular machinery.

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Scientists find ways to pick a protein’s pockets

Folded protein
This graphic shows the structure of a computationally designed protein that incorporates sheet-like structures with pockets, known as beta sheets. The beta sheets are the wavy “noodles” in the diagram. The structure also incorporates curled-up molecular spirals. (UW Institute for Protein Design / AAAS)

Researchers at the University of Washington have cracked the code for producing molecular structures with tiny pockets – structures that are likely to expand the repertoire for custom-designed proteins.

The structures, technically known as beta sheets, are thought to have an effect on metabolic pathways and cell signaling. Knowing how to produce them synthetically in precise configurations could lead to new treatments for maladies such as AIDS, cancer and Alzheimer’s disease.

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Scientists add twists to protein designs

Image: Protein molecule
A model shows a protein molecule with a hydrogen-bond network. (Credit: Boyken et al. / Science)

Biochemists from the University of Washington have engineered complex protein molecules with additional chemical bonds that make it possible to mix and match them like the base pairs of DNA.

The designer proteins, described today in a paper published by the journal Science, could open the way for a kind of synthetic coding system modeled after the groundbreaking double-helix DNA code system discovered by James Watson and Francis Crick back in 1953.

“Think of it this way: The principle of heredity is Watson-Crick base pairing between the two complementary strands of DNA. We invent in the paper an analogous pairing arrangement for proteins,” David Baker, director of the UW’s Institute for Protein Design, told GeekWire in an email.

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Designer proteins open up biotech frontiers

Image: Protein design
Computational designs for proteins can be turned into molecular models like the one at left, or into actual molecules with medical applications. (Credit: UW Institute for Protein Design)

Synthetic genomes and gene editing are big things today, but the next big things in biotechnology could be proteins that are designed and edited on computers – and are then synthesized to produce novel types of medicines, materials and molecular machines.

“It’s the right time for this field,” David Baker, director of the University of Washington’s Institute for Protein Design, said Monday at the EXOME Life Science Disruptors conference. The event was presented by Xconomy at the Fred Hutchinson Cancer Research Center in Seattle.

Baker is a pioneer in protein design, going back to the invention of the Rosetta protein modeling software more than a decade ago. Rosetta spawned the Foldit video game, which has attracted hundreds of thousands of protein-folding players. It has also spawned a commercial spin-out known as Cyrus Biotechnology, which is turning Rosetta into a commercial-grade, cloud computing platform.

“We are currently doing projects with eight companies, have four companies about to start a paid beta test … and a growing wait list to enter the beta, currently two companies,” Cyrus Biotech CEO Lucas Nivón told GeekWire in an email. “The next big events on Cyrus’s horizon are the official launch of beta in mid-May, and the launch out of beta into initial release in the June/July time frame.”

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