Featured Research

from universities, journals, and other organizations

Protein data bank archives its 100,000th molecule structure

Date:
May 14, 2014
Source:
University of California, San Diego
Summary:
As the single worldwide repository for the three-dimensional structures of large molecules and nucleic acids that are vital to pharmacology and bioinformatics research, the Protein Data Bank (PDB) recently archived its 100,000th molecule structure, doubling its size in just six years.

The number of structures available in the PDB per year, as of May 14, 2014. Highlighted examples include myoglobin (1; PDB ID 1mbn), the first structure solved by X-ray crystallography, and small enzymes (2; top: 4pti, bottom right: 2cha, bottom left: 3cpa). As technologies developed, the archive grew to host examples of tRNA (3; 6tna), viruses (4; 4rhv), antibodies (5; 1igt), protein-DNA complexes (6; top to bottom, 1j59, 1tro, 2bop, 1aoi), ribosomes (7; 1fjg, 1fka, 1ffk), and chaperones (8; 1aon).
Credit: Image courtesy of wwPDB

As the single worldwide repository for the three-dimensional structures of large molecules and nucleic acids that are vital to pharmacology and bioinformatics research, the Protein Data Bank (PDB) recently archived its 100,000th molecule structure, doubling its size in just six years.

Four data centers, including one co-located at Rutgers, The State University of New Jersey; and the San Diego Supercomputer Center (SDSC)/Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, support online access to the three-dimensional structures of biological macromolecules that help researchers understand many facets of biomedicine, agriculture, and ecology, from protein synthesis to health and disease to biological energy.

Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached this critical milestone thanks to the efforts of structural biologists throughout the world.

"The PDB is a critical resource for the international community of working scientists which includes everyone from geneticists to pharmaceutical companies interested in drug targets," said Nobel Laureate Venki Ramakrishnan, of the MRC Laboratory of Molecular Biology in Cambridge, England.

"SDSC has provided safe haven for the PDB since it arrived at UC San Diego in the late 1990s, along with Phil Bourne," said SDSC Director Michael Norman. "It was the project that initially got us involved in data science, and it remains an important element in our 'Big Data' strategy. I congratulate the PDB project for their success and achieving this significant milestone."

Bourne recently joined the National Institutes of Health as the Associate Director for Data Science. He formerly was Associate Vice Chancellor for Innovation and Industry Alliances, a Professor in the Department of Pharmacology and Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego, an SDSC Distinguished Scientist, as well as Associate Director of the RCSB (Research Collaboratory for Structural Bioinformatics) PDB.

Function Follows Form

In the 1950s, scientists had their first direct look at the structures of proteins and DNA at the atomic level. Determination of these early three-dimensional structures by X-ray crystallography ushered in a new era in biology -- one driven by the intimate link between form and biological function. As the value of archiving and sharing these data was quickly recognized by the scientific community, the PDB was established as the first open access digital resource in all of biology by an international collaboration in 1971, with data centers located in the U.S. and the United Kingdom.

Among the first structures deposited in the PDB were those of myoglobin and hemoglobin, two oxygen-binding molecules whose structures were elucidated by Chemistry Nobel Laureates John Kendrew and Max Perutz. With this week's regular update, the PDB welcomes 219 new structures into the archive. These structures join others vital to drug discovery, bioinformatics, and education, for a total of 100,147 entries.

The PDB releases approximately 200 new structures to the scientific community every week. The resource is accessed hundreds of millions of times annually by researchers, students, and educators intent on exploring how different proteins are related to one another, to clarify fundamental biological mechanisms and discover new medicines.

Future Challenges

As the scientific community eagerly awaits many more structures to be deposited in the PDB along with the invaluable knowledge these additions will bring, the increasing number, size, and complexity of that data constitute major challenges for the management of the archive. The wwPDB earlier this year launched a new Deposition and Annotation System designed to meet the evolving needs of the scientific community over the next decade. Since its initial launch, more than 750 X-ray crystallographic structures from 30 countries have been deposited using the new system.


Story Source:

The above story is based on materials provided by University of California, San Diego. The original article was written by Jan Zverina. Note: Materials may be edited for content and length.


Cite This Page:

University of California, San Diego. "Protein data bank archives its 100,000th molecule structure." ScienceDaily. ScienceDaily, 14 May 2014. <www.sciencedaily.com/releases/2014/05/140514153115.htm>.
University of California, San Diego. (2014, May 14). Protein data bank archives its 100,000th molecule structure. ScienceDaily. Retrieved August 21, 2014 from www.sciencedaily.com/releases/2014/05/140514153115.htm
University of California, San Diego. "Protein data bank archives its 100,000th molecule structure." ScienceDaily. www.sciencedaily.com/releases/2014/05/140514153115.htm (accessed August 21, 2014).

Share This




More Plants & Animals News

Thursday, August 21, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Drug Used To Treat 'Ebola's Cousin' Shows Promise

Drug Used To Treat 'Ebola's Cousin' Shows Promise

Newsy (Aug. 21, 2014) — An experimental drug used to treat Marburg virus in rhesus monkeys could give new insight into a similar treatment for Ebola. Video provided by Newsy
Powered by NewsLook.com
Terrifying City-Dwelling Spiders Are Bigger And More Fertile

Terrifying City-Dwelling Spiders Are Bigger And More Fertile

Newsy (Aug. 21, 2014) — According to a new study, spiders that live in cities are bigger, fatter and multiply faster. Video provided by Newsy
Powered by NewsLook.com
Lost Brain Cells To Blame For Sleep Problems Among Seniors

Lost Brain Cells To Blame For Sleep Problems Among Seniors

Newsy (Aug. 21, 2014) — According to a new study, elderly people might have trouble sleeping because of the loss of a certain group of neurons in the brain. Video provided by Newsy
Powered by NewsLook.com
Ramen Health Risks: The Dark Side of the Noodle

Ramen Health Risks: The Dark Side of the Noodle

AP (Aug. 21, 2014) — South Koreans eat more instant ramen noodles per capita than anywhere else in the world. But American researchers say eating too much may increase the risk of diabetes, heart disease and stroke. (Aug. 21) Video provided by AP
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:
from the past week

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