Navigation Links
Computers close in on protein structure prediction

and the protein backbone, the computer then uses a detailed physical chemistry based force field which favors close packing of atoms and hydrogen bonding to more accurately compute the energy of the structure.

"What seems to be critical is the packing of the molecule," Baker said. "The protein fits together perfectly with no holes in the middle, and no atoms on top of each other. It's about as densely packed as it could be. It's like a three-dimensional jigsaw puzzle."

The researchers upped their odds of finding the right match by repeating the two-step process with 50 homologs of the proteins from other genomes, such as a mouse or fly. The protocol was first tested on a blind annual prediction test considered to be the highest standard for removing bias from protein structure prediction models.

"We can't compute the energies perfectly, but the biggest problem is the search through possible shapes," Baker said. "Where we were not getting the right answer on the computer, it was almost always the case that the actual structure had the lowest energy, so we would have succeeded if we had explored this part of the space."

In a related paper published in the August issue of the journal Proteins, Baker and his colleagues reported that similar approaches can be used to predict the structures of protein complexes. "For the first time, computational methods are able, for a subset of cases, to produce really accurate models," he said.

Baker compares the computer simulations of the proteins to the problem of trying to find the lowest point on the surface of the Earth for the first time. A simple way to find the lowest place on the planet is to send out as many explorers as possible. The more explorers there are the more likely one of them is to stumble onto the shoreline of the Dead Sea ?the Earth's lowest point on land not covered by water. Each of the thousands of computer simulations is like one explorer.

Although the 33 per
'"/>

Source:Howard Hughes Medical Institute


Page: 1 2 3 4

Related biology news :

1. Computers to be used to find blueprint for new influenza drug
2. Computers to save unique type of American red squirrel
3. Chemicals in tattoo inks need closer scrutiny
4. Doctors closer to using gene analysis to help trauma patients
5. Proteomics brings researchers closer to understanding microbes that produce acid mine drainage
6. New results validating Pall prion reduction filter disclosed at ISBT Congress
7. Scientists closer to new cancer detection method
8. Getting close to nature is good for you
9. Scientists observe how a close bond activates the immune system
10. Stroke treatment a step closer after trial
11. Multiple genes permit closely related fish species to mix and match their color vision
Post Your Comments:
*Name:
*Comment:
*Email:
TAG: Computers close protein structure prediction

(Date:7/11/2014)... German . ... refraction of X-rays through a specimen instead of attenuation ... are often of much higher quality than those based ... Franz Pfeiffer are particularly interested in developing new approaches ... phase-contrast imaging. One main goal is to make this ...
(Date:7/11/2014)... July 3, 2014, Shenzhen, China Researchers from Salk ... for the first time evaluated the safety and ... and successfully developed a new method, TALEN-HDAdV, which ... pluripotent stem cell (hiPSC). This study published online ... important theoretical foundation for stem cell-based gene therapy. ...
(Date:7/11/2014)... July 11, 2014 Researchers have pioneered a ... The new technology, called Virtual Finger, allows scientists ... like neurons and synapses using the flat surface ... makes 3D imaging studies orders of magnitude more ... unprecedented level across many areas of experimental biology. ...
Breaking Biology News(10 mins):New simple setup for X-ray phase contrast 2A new genome editing method brings the possibility of gene therapies closer to reality 2Virtual finger enables scientists to navigate and analyze complex 3D images 2
... reservoirs and groundwater as well as snow fields and ... terrestrial life and human livelihoods. Continuous observations are ... of mankind and the environment and also to provide ... floods and droughts. These tasks are routinely undertaken by ...
... isolation have been traced to altered levels of an enzyme ... done in mice by researchers at the University of Illinois ... online addition of the Proceedings of the National Academy of ... stress because social isolation in both animals and humans can ...
... Athens, Ga. Parasites can decimate amphibian populations, but one ... role in spurring the evolution of new and sometimes bizarre ... Odum School of Ecology Savannah River Ecology Lab, explains that ... good example), and then make their way onto land as ...
Cached Biology News:Space technology put into service for global water resources observations 2Effects of social isolation traced to brain hormone 2Parasites might spur evolution of strange amphibian breeding habits 2
(Date:7/10/2014)... Calabasas, CA (PRWEB) July 10, 2014 ... academic institutions and professional associations, addressed the challenges of ... & Medical Device Industries” through strategic sourcing. Describing the ... ) with the Supply Chain Management Institute ( SCMI) ... the event on June 24 at the Kroc Institute ...
(Date:7/10/2014)... 2014  Kainos Capital, a firm specializing in acquiring ... it has acquired the Slim-Fast brand from Unilever. Unilever ... of the transaction were not disclosed. Slim-Fast ... that markets ready-to-drink shakes, powders, bars and snacks to ... and in the United Kingdom ...
(Date:7/10/2014)... Ceres, Inc . (Nasdaq: CERE ), an ... for the three months ended May 31, 2014 and ... reported that the company and its customers have made ... Brazil, which concluded in June, despite dry and hot ... part of the growing season. Yields of several of ...
(Date:7/10/2014)... WASHINGTON D.C., June 17, 2014 Using microscopic ... of specific gases, researchers at MIT,s Quantum Photonics ... detection levels in the parts-per-billion range. Optical sensors ... to their high signal-to-noise ratio, compact, lightweight nature, ... optical gas sensors had been developed before, the ...
Breaking Biology Technology:Biotech & Biopharm Supply Chain Management Executives Launch BSMA in San Diego 2Biotech & Biopharm Supply Chain Management Executives Launch BSMA in San Diego 3Biotech & Biopharm Supply Chain Management Executives Launch BSMA in San Diego 4Kainos Capital Acquires Slim-Fast From Unilever 2Ceres Announces Fiscal Third Quarter 2014 Financial Results 2Ceres Announces Fiscal Third Quarter 2014 Financial Results 3Ceres Announces Fiscal Third Quarter 2014 Financial Results 4Ceres Announces Fiscal Third Quarter 2014 Financial Results 5Ceres Announces Fiscal Third Quarter 2014 Financial Results 6Ceres Announces Fiscal Third Quarter 2014 Financial Results 7Ceres Announces Fiscal Third Quarter 2014 Financial Results 8Ceres Announces Fiscal Third Quarter 2014 Financial Results 9Swell new sensors 2
... Myriant Corporation today announced the successful development ... chemicals, including succinic acid and both L(+) and ... (Logo: http://photos.prnewswire.com/prnh/20110531/NE11071LOGO) "Today,s announcement ... to continue driving the advancement and global use ...
... October 5, 2011 Elsevier, a world-leading ... services, and the University of Sydney, Australia,s leading higher ... the 24-hour Sydney Hackathon . ... developed software applications to improve delivery of scientific, medical ...
... Technologies Corporation (NASDAQ: LIFE ) announced today it ... October 25, 2011, after market close. The company will also ... ET to discuss operating results, as well as future expectations. ... webcast can be accessed through the investor relations page of ...
Cached Biology Technology:Myriant Produces Succinic Acid and Lactic Acid From Non-Food Cellulosic Feedstocks 2Elsevier and the University of Sydney Announce Prize Winners of 24-Hour Hackathon 2Elsevier and the University of Sydney Announce Prize Winners of 24-Hour Hackathon 3Elsevier and the University of Sydney Announce Prize Winners of 24-Hour Hackathon 4Elsevier and the University of Sydney Announce Prize Winners of 24-Hour Hackathon 5Life Technologies Sets 3rd Quarter 2011 Earnings Release Date for Tuesday, October 25, 2011 2
... VSN-5 Nutating Mixer is a combination of ... a three dimensional action while providing gentle, ... quality unit can be used for a ... of specimens, tissue culture, immunoblots, staining/destaining, chromatography, ...
... The FastPlax Titer Kit is designed for determination ... of 46 days as in other methods. Classical ... appearance of plaques, but the FastPlax Kit takes ... AcNPV gp64 glycoprotein on the cell surface as ...
... Thermocycler combines top performance with exquisite design. ... speed and unparalleled temperature uniformity. The instrument ... in a spreadsheet or alternatively in a ... opens on the push of a button ...
...
Biology Products: