Press Archive

SDSC'S NBCR Project Hosts BioSync Web Site To Provide Information and Scheduling For Synchroton Resources World Wide

Published 08/04/1999

Media Contact: David Hart, (858) 534-8314, dhart@sdsc.edu

The National Center for Research Resources at the National Institutes of Health has funded the National Biomedical Computation Resource (NBCR) at the San Diego Supercomputer Center (SDSC) to develop a Web site for BioSync, the Structural Biology Synchrotron Users Organization. The site began operating this week at http://biosync.sdsc.edu/ as a portal for investigators planning visits to synchrotron facilities and as a central resource for researchers in structural biology seeking information about such facilities.

Knowledge of the structure of biological macromolecules is key to understanding their functioning in biological systems, and synchrotron x-ray crystallography has helped to unravel the structures of ever-larger and more complex molecules. Fully half of the new 3-D structures deposited in the Protein Data Bank (PDB) are based on studies done at one of a dozen such facilities worldwide.

Until recently, however, biologists who wished to use synchrotrons have been on their own when answering questions about the facilities, the beam characteristics, the equipment on site and that which must be provided by the researcher, as well as scheduling and travel information. The BioSync Web site now puts all that information at researchers' fingertips.

The site was announced today at the annual meeting of the International Union of Crystallography in Glasgow, Scotland, by Janet L. Smith of Purdue University, who chairs BioSync. The members of BioSync include about 500 leaders of research groups in structural biology.

"Our new Web site contains detailed information about high-energy synchrotron facilities used for x-ray diffraction studies of the three-dimensional structure of biological molecules," Smith said. "This will demystify what has been a 'word of mouth' process and help to rationalize and democratize the use of the facilities. Everything one needs to know will be there, including places to stay while conducting research at a synchrotron."

There are five major synchrotron facilities in the United States, four operated by the Department of Energy (DOE) and one operated by NSF, and several new facilities are being built. In addition, facilities abroad are also available to U.S. researchers. The BioSync Web site has links to all the U.S. facilities (which include 24 separate beam lines for various purposes) and to nine other facilities in Europe, Japan, and South America.

"I'm very pleased that NBCR is hosting and maintaining this site," said John Wooley, newly appointed Associate Vice Chancellor for Research at the University of California, San Diego (UCSD). "The site represents a real service to the structural biology community and an important addition to the constellation of biological research resources being assembled at and around UCSD."

That sentiment was echoed by Peter Arzberger, executive director of SDSC and director of NBCR. "Our NIH Research Resource is devoted to problems in computational biology, and the analysis of macromolecular structure comprises much of what we do," Arzberger said. "Since the initial data for so many structures is obtained at synchrotron facilities, the BioSync Web site located here is well within our service mission." NBCR facilitates biomedical research by providing investigators with easy access to advanced computational and visualization capabilities via the Web.

The idea for hosting the site originated with SDSC's Phil Bourne, who leads an NBCR project pursuing A Data-Management Environment for Multiscale Biological Modeling. He and SDSC colleague John Badger worked with Janet Smith and a team from NIH to obtain the supplemental funding necessary to build the Web site.

Over the past 10 years, the use of high-energy synchrotron beams in x-ray crystallography has grown rapidly, according to BioSync research. In 1990, a survey estimated that about 15 percent of new structures deposited in the PDB were solved in part using synchrotron facilities. In the early 1990s, that figure jumped to 25 percent. "Four or five years ago, new facilities began to come on line," Smith said, "and new cryotechnology for preserving crystals meant that many more structures could be studied." According to BioSync's survey, about half of the 500 new protein structures found and registered in the PDB in 1997 involved data initially obtained at synchrotron facilities.

"The great advantage of the synchrotron x-ray facilities over traditional laboratory x-ray sources is that the lab sources are usually monochromatic, radiating at one wavelength only, while the synchrotron beams are both many times more intense and also tunable to various wavelengths," said Christopher M. Smith, assistant director of NBCR. "By hosting the BioSync Web site and promoting access to synchrotron facilities, NBCR will be assisting structural biology research generally." The site is maintained by Anne Kuller of NBCR ( akuller@sdsc.edu).

The NBCR ( http://nbcr.sdsc.edu/) is funded by National Center for Research Resources at the NIH and is headquartered at SDSC ( http://www.sdsc.edu/), a research unit of the University of California, San Diego, and the leading-edge site of the National Partnership for Advanced Computational Infrastructure (NPACI, http://www.npaci.edu/). NPACI unites 46 universities and research institutions to build the computational environment for tomorrow's scientific discovery.