APPLICATIONS

The National Science Foundation (NSF) has awarded more than $1 million for research at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego to develop the Protein Kinase Resource, a database cataloging a family of enzymes that play key roles in cellular regulation. Under development at SDSC since 1996, the existing Protein Kinase Resource (http://pkr.sdsc.edu) will be extended to create a resource from which both novices and experts can learn about protein kinases, an important family of enzymes that play roles in processes as diverse as human disease and crop production. More than 10,000 visitors per week currently use the resource, which contains 11,430 entries. The NSF award, totaling $1.18 million over three years, will be used to integrate the Protein Kinase Resource with other databases and to build a detailed and well-defined application program interface. "Our goal is to build a system that is narrowly focused on protein kinases, protein phosphatases, and related molecules," said Michael Gribskov, the project principal investigator who is a computational biologist at SDSC and adjunct associate professor of biology at UCSD. "In contrast to major databases that are publicly available today—such as GenBank and the Protein Data Bank—we are producing a system with information that runs deeply, rather than broadly, to provide biomedical researchers with powerful tools for scientific discovery." Susan Taylor, professor of chemistry and biochemistry at UCSD, serves as co-principal investigator on the Protein Kinase Resource project. "The next generation of scientific advances will be the result of the coordination of technical expertise and the ability to use and leverage large-scale computational and data management infrastructure," said Fran Berman, director of SDSC and the National Partnership for Advanced Computational Infrastructure. "The PKR project is an excellent example of the use of technology to enable 21st century science." The award is the latest in a series of grants establishing or expanding biological database repositories at SDSC. Other well-known databases housed at SDSC include the Protein Data Bank (the worldwide repository for the processing and distribution of 3-D biological macromolecular structure data, http://www.pdb.org), PlantsT (a database of functional genomics of plant transporters, http://plantst.sdsc.edu), and PlantsP (a database of functional genomics of plant phosphorylation, http://plantsp.sdsc.edu). The human genome contains more than 500 protein kinases, which are primarily known as messengers that carry signals—both between and within cells. Kinases trigger events such as new blood vessel growth, metabolic changes, and programmed cell death. According to Gribskov, protein kinases serve as a testbed for the development of biological information systems because they act as switches in the cellular metabolism, which can be correlated to the abundance of sequence, structural, disease, and genetic data available about them.