Featured Research

from universities, journals, and other organizations

Discarded data may hold the key to a sharper view of molecules

Date:
May 24, 2012
Source:
Oregon State University
Summary:
There's nothing like a new pair of eyeglasses to bring fine details into sharp relief. For scientists who study the large molecules of life from proteins to DNA, the equivalent of new lenses have come in the form of an advanced method for analyzing data from X-ray crystallography experiments.

There's nothing like a new pair of eyeglasses to bring fine details into sharp relief. For scientists who study the large molecules of life from proteins to DNA, the equivalent of new lenses have come in the form of an advanced method for analyzing data from X-ray crystallography experiments.

Related Articles


The findings, just published in the journal Science, could lead to new understanding of the molecules that drive processes in biology, medical diagnostics, nanotechnology and other fields.

Like dentists who use X-rays to find tooth decay, scientists use X-rays to reveal the shape and structure of DNA, proteins, minerals and other molecules.

As X-rays pass through atoms, they reflect distinctive patterns, which reveal what atoms are present and how atoms are bonded to each other. However, some data are typically discarded because of concerns over quality. In particular, data derived from edge regions of the pattern -- although very important for understanding the details of structure -- are often overwhelmed by the random errors associated with a weak signal in the midst of a lot of background noise.

Oregon State University biophysicist Andy Karplus and his colleague Kay Diederichs at the University of Konstanz in Germany have now proven that useful information can be gleaned from data that have about five times the noise level that was previously considered acceptable.

"The criteria that have been used in the past are way too conservative," said Karplus, an expert in protein structure and stability. "These data that people have been throwing out are actually good."

The bottom line for crystallographers is the accuracy of their molecular models. The better the model, the better it will predict the pattern created by X-rays passing through a molecule, and the better it will be to develop new drugs and nanotechnologies that operate at the molecular scale.

The new method may be the most important conceptual advance in the past 20 years in how these data are used in modeling, the scientists said. It shows how data from "noisy" parts of the measurement can still provide information and allows scientists to see directly where the model is limited by noise in the data and where the model is a better estimate of molecular structure than experimental data.

"The question is, 'Where do we cut it off?'" said Karplus. By adding data at incremental steps and showing how the model improved, Karplus and Diederichs showed that scientists had been cutting off their analyses too soon and discarding data that could sharpen their view of molecular structure.

"The big impact on the field will be that every structure determined from here on out will be a little more accurate because people won't throw away data that are okay," Karplus said. "If you have a crummy image of the protein, it will get a little sharper. If you have a good image of the protein, it will also get a little sharper."

While the method will be an important step for X-ray crystallographers, the scientists said that other physical sciences may also find ways to benefit from this type of data quality analysis. They noted that one branch of science has been using this type of statistical analysis for many years. The field of psychometrics -- the analysis of data from psychological tests -- has used a similar technique called the "Spearman-Brown prophecy formula" to determine the minimum length of such tests.

"Now that we know that very noisy data are useful, this will presumably enable still further improvements as it stimulates new software development to do a better job of handling such weak data," said Karplus.


Story Source:

The above story is based on materials provided by Oregon State University. Note: Materials may be edited for content and length.


Journal Reference:

  1. P. A. Karplus, K. Diederichs. Linking Crystallographic Model and Data Quality. Science, 2012; 336 (6084): 1030 DOI: 10.1126/science.1218231

Cite This Page:

Oregon State University. "Discarded data may hold the key to a sharper view of molecules." ScienceDaily. ScienceDaily, 24 May 2012. <www.sciencedaily.com/releases/2012/05/120524143527.htm>.
Oregon State University. (2012, May 24). Discarded data may hold the key to a sharper view of molecules. ScienceDaily. Retrieved April 21, 2015 from www.sciencedaily.com/releases/2012/05/120524143527.htm
Oregon State University. "Discarded data may hold the key to a sharper view of molecules." ScienceDaily. www.sciencedaily.com/releases/2012/05/120524143527.htm (accessed April 21, 2015).

Share This


More From ScienceDaily



More Matter & Energy News

Tuesday, April 21, 2015

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Humanoid Robot Can Recognise and Interact With People

Humanoid Robot Can Recognise and Interact With People

Reuters - Innovations Video Online (Apr. 20, 2015) An ultra-realistic humanoid robot called &apos;Han&apos; recognises and interprets people&apos;s facial expressions and can even hold simple conversations. Developers Hanson Robotics hope androids like Han could have uses in hospitality and health care industries where face-to-face communication is vital. Matthew Stock reports. Video provided by Reuters
Powered by NewsLook.com
Drones and Health Apps at Santiago's "Robotics Day"

Drones and Health Apps at Santiago's "Robotics Day"

AFP (Apr. 20, 2015) Latin American robotics experts gather in Santiago, Chile for "Robotics Day". Video provided by AFP
Powered by NewsLook.com
Japan Humanoid Robot Receives Customers at Department Store

Japan Humanoid Robot Receives Customers at Department Store

AFP (Apr. 20, 2015) She can smile, she can sing and she can give you guidance at one of the most upscale department stores in Tokyo...a female-looking humanoid makes her debut as a receptionist Video provided by AFP
Powered by NewsLook.com
Pee-Power Toilet to Light Up Disaster Zones

Pee-Power Toilet to Light Up Disaster Zones

Reuters - Innovations Video Online (Apr. 20, 2015) Students and staff are being asked to use a prototype urinal to &apos;donate&apos; urine to fuel microbial fuel cell (MFC) stacks that generate electricity to power lighting. The developers hope the pee-power technology will light toilet cubicles in refugee camps, where women are often at risk of assault in poorly lit sanitation areas. Matthew Stock reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Space & Time

Matter & Energy

Computers & Math

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins