News

A consortium of scientists managing the Protein Data Bank (PDB) - the world's central online archive containing detailed structural data on proteins, nucleic acids, and protein-nucleic acid complexes - has released a software toolkit that provides more seamless access to this information. The OpenMMS (Open Macromolecular Structure) Toolkit, released by the nonprofit Research Collaboratory for Structural Bioinformatics (RCSB) consortium, allows researchers to use the PDB more efficiently with the Common Object Request Broker Architecture (CORBA) standard. The CORBA specification provides a standard application programming interface that allows remote programs direct access to the detailed experimental and macromolecular data available in the PDB.

Researchers rely on the PDB to pursue a wide range of biological investigations, such as drug discovery and design, molecular comparison analysis, and studies of evolution at the molecular level. "The RCSB consortium is committed to providing PDB data in the most effective way possible, and the newly released alpha version of the OpenMMS toolkit does that," said Philip Bourne, co-director of RCSB and director of Integrated Biosciences at the San Diego Supercomputer Center (SDSC), and professor of Pharmacology at the University of California, San Diego.

Douglas Greer, a principal scientist at SDSC, designed and wrote the OpenMMS toolkit software. It contains programs for parsing data stored in the standard Macromolecular Crystallographic Information File (mmCIF) format. The toolkit also contains software for loading mmCIF data files into a relational database, translating the data into an XML-formatted file, and running a CORBA server to deliver binary MMS data directly over a network connection to local or remote applications. The software also allows researchers to create customized software to utilize PDB information in novel ways to their specifications. The translation into the different formats is driven by a central metamodel based on the mmCIF dictionary.

All of the software for the metamodel and for generating the translated expressions is written in Java and is included with the distributions, which can be run on any Java-enabled operating system. The technical development effort was led by Bourne and John D. Westbrook, co-director of the RCSB and associate research professor at Rutgers University.

The RCSB consortium is led by Rutgers University, SDSC, and the National Institute of Standards and Technology. Funding for the OpenMMS project was provided by the National Science Foundation and the National Partnership for Advanced Computational Infrastructure.

The San Diego Supercomputer Center (SDSC) is an organized research unit of the University of California, San Diego, and the leading-edge site of the National Partnership for Advanced Computational Infrastructure (NPACI). SDSC's mission is to develop and use technology to advance science, and SDSC provides leadership both nationally and internationally in computing, data management, biosciences, and other areas. As a national laboratory for computational science and engineering, SDSC is funded by the National Science Foundation through NPACI and other federal agencies, the state, the University of California, and private organizations. For more information, see www.sdsc.edu or contact David Hart, SDSC Communications, (858) 534-8314, dhart@sdsc.edu

Media Contacts:

Tammy Battistuz, Protein Data Bank, 858-534-8355, tammyb@sdsc.edu

David Hart, SDSC Communications, 858-534-8314, tammyb@sdsc.edu