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Accurate protein structure prediction now accessible to all: New artificial intelligence software can compute protein structures in 10 minutes – Science Daily

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Scientists have waited months for access to highly accurate protein structure prediction since DeepMind presented remarkable progress in this area at the 2020 Critical Assessment of Structure Prediction, or CASP14, conference. The wait is now over.

Researchers at the Institute for Protein Design at the University of Washington School of Medicine in Seattle have largely recreated the performance achieved by DeepMind on this important task. These results will be published online by the journal Science on Thursday, July 15.

Unlike DeepMind, the UW Medicine team’s method, which they dubbed RoseTTAFold, is freely available. Scientists from around the world are now using it to build protein models to accelerate their own research. Since July, the program has been downloaded from GitHub by over 140 independent research teams.

Proteins consist of strings of amino acids that fold up into intricate microscopic shapes. These unique shapes in turn give rise to nearly every chemical process inside living organisms. By better understanding protein shapes, scientists can speed up the development of new treatments for cancer, COVID-19, and thousands of other health disorders.

“It has been a busy year at the Institute for Protein Design, designing COVID-19 therapeutics and vaccines and launching these into clinical trials, along with developing RoseTTAFold for high accuracy protein structure prediction. I am delighted that the scientific community is already using the RoseTTAFold server to solve outstanding biological problems,” said senior author David Baker, professor of biochemistry at the University of Washington School of Medicine, a Howard Hughes Medical Institute investigator, and director of the Institute for Protein Design.

In the new study, a team of computational biologists led by Baker developed the RoseTTAFold software tool. It uses deep learning to quickly and accurately predict protein structures based on limited information. Without the aid of such software, it can take years of laboratory work to determine the structure of just one protein.

RoseTTAFold, on the other hand, can reliably compute a protein structure in as little as ten minutes on a single gaming computer.

The team used RoseTTAFold to compute hundreds of new protein structures, including many poorly understood proteins from the human genome. They also generated structures directly relevant to human health, including those for proteins associated with problematic lipid metabolism, inflammation disorders, and cancer cell growth. And they show that RoseTTAFold can be used to build models of complex biological assemblies in a fraction of the time previously required.

RoseTTAFold is a “three-track” neural network, meaning it simultaneously considers patterns in protein sequences, how a protein’s amino acids interact with one another, and a protein’s possible three-dimensional structure. In this architecture, one-, two-, and three-dimensional information flows back and forth, thereby allowing the network to collectively reason about the relationship between a protein’s chemical parts and its folded structure.

“We hope this new tool will continue to benefit the entire research community,” said Minkyung Baek, a postdoctoral scholar who led the project in the Baker laboratory at UW Medicine.

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'There is contact!': Russia's new Nauka space module docks with ISS – Ottawa Sun

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MOSCOW — Russia upgraded its capabilities on the International Space Station on Thursday after its new Nauka module, set to serve as a research lab, storage unit and airlock, successfully docked with it after a nervy journey from Earth.

A live broadcast from Russia’s space agency, Roscosmos, showed the module, a multipurpose laboratory named after the Russian word for ‘science’, docking with the ISS at 1329 GMT, a few minutes later than scheduled.

“According to telemetry data and reports from the ISS crew, the onboard systems of the station and the Nauka module are operating normally,” Roscosmos said in a statement.

“There is contact!!!” Dmitry Rogozin, the head of Roscosmos, wrote on Twitter moments after the docking.

Since it launch last week from Kazakhstan’s Baikonur Cosmodrome, the module had suffered a series of glitches that had raised concerns about whether the docking procedure would go smoothly.

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Thursday’s development suggests Russia is interested in maintaining the ISS despite previous comments from Rogozin who last month suggested Moscow would withdraw from it in 2025 unless Washington lifted sanctions on the space sector that he said were hampering Russian satellite launches.

Launched in 1998, the ISS is a multinational project and comprises two segments, a Russian one and another one used by the United States and other space agencies.

“After its commissioning, the Russian segment will receive additional room for arranging workplaces, storing cargo and housing water and oxygen regeneration equipment,” Roscosmos said its statement.

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Russian module knocks International Space Station out of position – Euronews

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A Russian module knocked the International Space Station out of position briefly on Thursday, after it accidentally fired its thrusters.

For 47 minutes, the space station lost control of its orientation when the firing occurred a few hours after docking, pushing the orbiting complex from its normal configuration.

The station’s position is key for getting power from solar panels and or communications. Communications with ground controllers also blipped out twice for a few minutes.

Flight controllers regained control using thrusters on other Russian components at the station to right the ship, and it is now stable and safe, NASA said.

“We haven’t noticed any damage,” space station program manager Joel Montalbano said in a late afternoon press conference.

“There was no immediate danger at any time to the crew.”

Montalbano said the crew didn’t really feel any movement or any shaking. NASA said the station moved 45 degrees out of attitude, about one-eighth of a complete circle.

The complex was never spinning, NASA spokesman Bob Jacobs said.

NASA’s human spaceflight chief Kathy Lueders called it “a pretty exciting hour.”

The incident caused NASA to postpone a repeat test flight for Boeing’s crew capsule that had been set for Friday afternoon from Florida.

It will be Boeing’s second attempt to reach the 250-mile-high station before putting astronauts on board; software problems botched the first test.

Russia’s long-delayed 22-ton (20-metric-ton) lab called Nauka arrived earlier on Thursday, eight days after it launched from the Russian launch facility in Baikonur, Kazakhstan.

The launch of Nauka, which will provide more room for scientific experiments and space for the crew, had been repeatedly delayed because of technical problems. It was initially scheduled to go up in 2007.

In 2013, experts found contamination in its fuel system, resulting in a long and costly replacement. Other Nauka systems also underwent modernization or repairs.

Stretching 43 feet (13 meters) long, Nauka became the first new compartment for the Russian segment of the outpost since 2010.

On Monday, one of the older Russian units, the Pirs spacewalking compartment, undocked from the station to free up room for the new lab.

Nauka will require many maneuvers, including up to 11 spacewalks beginning in early September, to prepare it for operation.

The space station is currently operated by NASA astronauts Mark Vande Hei, Shane Kimbrough and Megan McArthur; Oleg Novitsky and Pyotr Dubrov of Russia’s Roscosmos space corporation; Japan Aerospace Exploration Agency astronaut Akihiko Hoshide and European Space Agency astronaut Thomas Pesquet.

In 1998, Russia launched the station’s first compartment, Zarya, which was followed in 2000 by another big piece, Zvezda, and three smaller modules in the following years. The last of them, Rassvet, arrived at the station in 2010.

Russian space officials downplayed the incident with Dmitry Rogozin, head of Roscosmos, tweeting: “All in order at the ISS. The crew is resting, which is what I advise you to do as well.”

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Warming Planet Means 83 Million Face Death From Heat This Century – Financial Post

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(Bloomberg) — A population equivalent to that of Germany — 83 million people — could be killed this century because of rising temperatures caused by greenhouse-gas emissions, according to a new study that might influence how markets price carbon pollution.

The research from Columbia University’s Earth Institute introduces a new metric to help companies and governments assess damages wrought by climate change. Accounting for the “mortality cost of carbon” could give polluters new reasons to clean up by dramatically raising the cost of emissions.

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“Based on the decisions made by individuals, businesses or governments, this tells you how many lives will be lost or saved,” said Columbia’s Daniel Bressler, whose research was published Thursday in the journal Nature Communications. “It quantifies the mortality impact of those decisions” by reducing questions down “to a more personal, understandable level.”

Read more: How Biden Is Putting a Number on Carbon’s True Cost: QuickTake 

Adapting models developed by Yale climate economist and Nobel Prize winner William Nordhaus, Bressler calculated the number of direct heat deaths that will be caused by current global-warming trajectories. His calculations don’t include the number of people who might die from rising seas, superstorms, crop failures or changing disease patterns affected by atmospheric warming. That means that the estimated deaths — which approximates the number of people killed in World War 2 — could still be a “vast underestimate,” Bressler said.

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Every 4,434 tons of carbon spewed in 2020 into the Earth’s atmosphere will kill one person this century, according to the peer-reviewed calculations that see the planet warming 4.1 degrees Celsius by 2100. So far the planet has warmed about 1.1 degrees Celsius, compared to pre-industrial times. 

The volume of pollution emitted over the lifetime of three average U.S. residents is estimated to contribute to the death of another person. Bressler said the highest mortality rates can be expected in Earth’s hottest and poorest regions in Africa, the Middle East and South Asia.

Read more: Life and Death in Our Hot Future Will be Shaped by Today’s Income Inequality

The new metric could significantly affect how economies calculate the so-called social cost of carbon, which U.S. President Joe Biden’s administration set at $51 a ton in February. That price on pollution, which complements carbon markets like the European Union’s Emissions Trading System, helps governments set policy by accounting for future damages. But the scale revealed by Bressler’s research suggests the social cost of carbon should be significantly higher, at about $258 a ton, if the world’s economies want to reduce deaths caused by global warming.

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A higher cost on carbon pollution could immediately induce larger emission cuts, which in turn could save lives. Capping global average temperature increase to 2.4 degrees Celsius by the end of the century, compared with modest emissions reductions that would warm the planet 3.4 degrees Celsius, could save 74 million people from dying of heat.

“People shouldn’t take their per-person mortality emissions too personally,” said Bressler. Governments need to mobilize “large-scale policies such as carbon pricing, cap and trade and investments in low carbon technologies and energy storage.”

©2021 Bloomberg L.P.

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