protein

Unipro's Ugene is a free bioinformatics modeling and visualization tool. You can use it to visualize, analyze, and annotate DNA and protein sequences. It's widely compatible with a variety of platforms, tools, and methods and includes an integrated Muscle alignment tool, integrated Hmmer2 package, an OpenGL viewer for PDB macromolecular structures, and a custom workflow designer.

Ugene isn't difficult to set up, though much of what it does depends on access to other files and tools. Ugene's functions are based around Projects, Tasks, and Logs. Under Application Settings, we could configure everything from system resource allocation … Read more

It's been a good year for video gamers--and not just the epic legions of Call of Duty fans enjoying Modern Warfare 3.

A few months after Foldit players helped decode the structure of a protein key to the way HIV multiplies, another group of gamers taking on DNA sequencing in the game Phylo have contributed more than 350,000 solutions, the game's designers at McGill University report.

When University of Washington researchers unveiled Foldit in 2008, it wasn't clear whether the protein-folding game would be a one hit wonder. But one-year-old Phylo, already averaging 1,000 eureka … Read more

It's not every day that a news item details the intelligence of the masses, lurking in the brains of unassuming passersby, just waiting to be uncovered for the greater good. But when it comes to the massively multiplayer online game Foldit, this is precisely the story, and it keeps getting better.

Launched in 2008 at the University of Washington, the protein folding game first made news for its potential to use the collective brainpower of gamers everywhere to unlock the fundamental mysteries of certain diseases. Then gamers began to prove this potential, solving various protein riddles that further our … Read more

In 2008, University of Washington scientists released the game Foldit, hoping a sort of critical mass of gamers would mess around with proteins and, in the process, uncover some of their intrigue. (We have more than 100,000 types of proteins in our bodies alone.)

Last year, we checked in on the project's progress, and principal investigator Zoran Popovic said that some 60,000 people worldwide had taken on the challenge. Popovic hoped the initial results his team reported on last year would convince those on the sidelines that scientific discovery games could actually lead to important breakthroughs.

Well, … Read more

The notion of erasing memories associated with painful or harmful pasts is not a new one. But it has remained just that: a notion.

Now scientists in Israel say they have devised a method to erase memories that trigger cravings in rats addicted to cocaine--a method that works so well it actually results in rats ignoring the place where they had been scoring the drug.

"Memories can trigger a desire for the drug, including memories of the drug itself, the needle, or the environment in which the drug was consumed," says Hebrew University researcher Rami Yaka. "This research indicates the possibility of erasing these memories in a way that will allow addicts to cancel the associations they have in their minds regarding the drug."

The team worked with a small protein called ZIP, which has been found in other studies in recent years to erase memories and even, as a result, inhibit learning processes.

After giving the rats cocaine in a designated spot in their pens for a few weeks, the team injected ZIP into the nucleus accumbens, a brain region known to control pleasure, reward, fear, and more, and then returned the rats to their pens. The rats proceeded to ignore the location they had only recently sought out, suggesting they no longer remembered either the place, the effect of the drug, or perhaps both.

Yaka, who will present his team's findings at the Facing Tomorrow 2011 conference in Jerusalem next week, sees possibilities not just for drug addicts but also those suffering from posttraumatic stress disorder and other psychological conditions.

Of course, it remains unclear whether the protein erases selective memories associated with drugs, or if other pleasure-and-reward memories are also affected. Will one also forget the sweetness of chocolate? The ecstasies of copulation? The kiss of a gentle summer's breeze?

If so, will it be worth it?… Read more

MEDFORD, Mass.--In this densely populated city outside Boston without a farm in sight, agriculture researchers are engineering corn and other crops to become better biofuels.

U.S. Secretary of Agriculture Tom Vilsack last week visited Agrivida, a small company working on a method it hopes will help deliver on the biofuels industry's promise of economically making fuel and chemicals from non-food crops. Vilsack toured the lab of Agrivida to draw attention to federal investments in renewable energy research and development.

Cheaper biofuels will help lower fuel costs and provide economic development in rural areas of the U.S., … Read more

Two professors at Binghamton University in New York are using a novel imaging technique to observe the behavior of an enzyme--called tubulin tyrosine ligase, or TTL--as its behavior can suggest whether certain cancer cells might grow more aggressively than others.

Though they are not developing actual therapies, Susan Bane and Susannah Gal say their research could help further personalize targeted cancer therapies.

"Potentially, we could put [a tumor sample] in our labeling system and say, 'Yes, that has a problem with the TTL system, and therefore you should be more aggressive with it,'" says Gal, whose work is funded by the National Institute of General Medical Sciences. "Or we could say, 'That's probably OK, so you can treat it with normal chemotherapy.'"

The enzyme TTL involves microtubules, which both help chromosomes line up correctly during cell division and provide part of the scaffolding of a cell's structure. Those microtubules are made of proteins called tubulin; the enzyme carboxypeptidase clips an amino acid called tyrosine off the ends of some of these proteins, and later the enzyme TTL puts that tyrosine back on.

Bane says it's unclear why tyrosine is clipped off only to be reattached, but it's clearly an important part of the cell's cycle: "We do know that if you don't have that enzyme, you'll die."

In some cancer cells, that cycle of removing and reattaching tyrosine is disrupted, with too many tubulins lacking tyrosine altogether. Tumors made of those cells, Bane says, "tend to grow more aggressively."… Read more

Since computer scientists and biochemists at the University of Washington launched a project in 2008 that taps into the brainpower of computer gamers to fold proteins, almost 60,000 people around the world have taken on the challenge.

In the process, Foldit players have been able to best computers on problems that require radical moves, risks, and long-term vision, according to results being published on Thursday, in the journal Nature.

"The really fundamental question in most scientists' minds was, 'What can it produce, in terms of results? Is there any evidence that it's doing something useful?'" says … Read more

CLC bio's Sequence Viewer is a free tool for basic bioinformatics analysis. It offers many of the features and capabilities of the publisher's high-end science software, such as the ability to perform many bioinformatics analyses, including interactive restriction site analysis, creating and editing alignments, phylogenetics, integrated GenBank searches, and advanced DNA to protein translation. It also carries over the premium utilities' sophisticated data management and exporting capabilities as well as compatibility with a wide range of platforms and file formats. It offers a continuously evolving lab-grade application in a compact, easy-to-use format that can access many integrated research … Read more