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International Collaborators to Form the Worldwide Protein Data Bank

Published 11/21/2003

Today the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database at the EMBL-European Bioinformatics Institute (MSD-EBI), and Protein Data Bank Japan (PDBj) announced a collaboration to form the Worldwide Protein Data Bank (wwPDB; The announcement is published in the December issue of Nature Structural Biology.

The collaboration reflects the growing international and interdisciplinary nature of scientific research, and formalizes the global character of the PDB, which has been used as an international resource for the collection and sharing of three-dimensional information on proteins and other large molecules since its inception 32 years ago. The formation of the wwPDB will be transparent to users and will ensure the overall quality and consistency of data directly available through the PDB.

"By providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that this wwPDB will allow for individual creativity in how the data are presented and made available to the community," said Helen Berman, director of the RCSB PDB and Board of Governors Professor of Chemistry at Rutgers, The State University of New Jersey.

Kim Henrick, head of the MSD-EBI said, "The PDB is a canonical research resource that transcends both scientific and political boundaries. The wwPDB agreement among the three equal partners elevates the responsibility for the deposition and accessibility of the data to a global level. The EBI has been a longtime deposition site and advisor to the PDB and the evolution of that role is a welcome development."

Head of the PDBj group at the Institute for Protein Research in Osaka University, Haruki Nakamura said, "The PDBj has become the representative for the PDB throughout Asia and Oceania. With the recent explosion of interest in structural biology and bioinformatics research in the region, which would not be possible without the PDB, it is a natural step for us to formalize our involvement through the wwPDB."

The PDB is the single archive of biological macromolecular structure data, which is made freely and publicly available to researchers, educators, and students. Worldwide, the PDB receives over 60 million hits per year. As of October 28, 2003, it contained 22,984 structures, a number that has been growing exponentially.

According to a 10-year agreement signed by the 3 founding members of the wwPDB, the sites will share responsibilities in data deposition, data processing, and distribution. An international advisory board will be formed to support the collaboration.

About the RCSB:

The RCSB PDB, operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology, is supported by funds from the National Science Foundation, the Department of Energy, and the National Institutes of Health.

Established in 1766, Rutgers is America's eighth oldest institution of higher learning and one of the nation's premier public research universities. Serving more than 50,000 students on campuses in Camden, Newark and New Brunswick/Piscataway, Rutgers offers more than 280 bachelor's, master's, doctoral and professional degree programs. The university is home to 29 degree-granting schools and colleges, and more than 150 specialized centers and institutes. With 320,000 living alumni, Rutgers graduates are major contributors to all sectors of contemporary life.

The San Diego Supercomputer Center's (SDSC) mission is to innovate, develop and deploy technology to advance science. SDSC is involved in an extensive set of collaborations and activities at the intersection of technology and science whose purpose is to enable and facilitate the next generation of scientific advances. Founded in 1985 and primarily funded by the National Science Foundation (NSF), SDSC is an organized research unit of the University of California, San Diego. With a staff of more than 400 scientists, software developers and support personnel, SDSC is an international leader in data management, biosciences, geosciences, grid computing and visualization.

The Center for Advanced Research in Biotechnology (CARB) is a partnership between the University of Maryland Biotechnology Institute (UMBI) and the National Institute of Standards and Technology (NIST). CARB conducts research and provides interdisciplinary training in fundamental problems at the forefront of biotechnology. Research at CARB centers on the structure, function, design and evolution of biological macromolecules, and relies on both theoretical and experimental approaches. One of CARB's primary goals is to cultivate a research environment that fosters the advancement of the local and national biotechnology industry. Its efforts are strengthened by collaborations with scientists at its parent institutions, as well as with trainees and visiting scientists. CARB is located on the University System of Maryland's Shady Grove Campus at the Shady Grove Life Science Center in Rockville, in the heart of Maryland's thriving biotechnology community.

About the EBI:

The MSD-EBI is supported by funds from the Wellcome Trust, the European Union (TEMBLOR, NMRQUAL, SPINE, AUTOSTRUCT, and IIMS awards), CCP4, the Biotechnology and Biological Sciences Research Council (UK), the Medical Research Council (UK), and the European Molecular Biology Laboratory.

The European Bioinformatics Institute (EBI) is part of the European Molecular Biology Laboratory (EMBL), and is located on the Wellcome Trust Human Genome Campus in Hinxton near Cambridge (UK). The EBI grew out of EMBL's pioneering work in providing public biological databases to the research community. It hosts some of the world's most important collections of biological data, including DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), animal genomes (Ensembl), three-dimensional structures (the Macromolecular Structure Database) and a new resource to hold data from microarray experiments (ArrayExpress). The EBI hosts several research groups and its scientists continually develop new tools for the biocomputing community.

About EMBL:

The European Molecular Biology Laboratory is a basic research institute funded by public research monies from 16 member states, including most of the EU, Switzerland and Israel. Research at EMBL is conducted by approximately 80 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and Outstations in Hinxton (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. The cornerstones of EMBL's mission are: to perform basic research in molecular biology, to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states, and to develop new instruments and methods in the life sciences. EMBL's international PhD Programme has a student body of about 170. The Laboratory also sponsors an active Science and Society programme. Visitors from the press and public are welcome.

About the PDBj:

Protein Data Bank Japan (PDBj) is supported by grant-in-aid from the Institute for Bioinformatics Research and Development, Japan Science and Technology Corporation (BIRD-JST), and the Ministry of Education, Culture, Sports, Science and Technology (MEXT).

PDBj was founded in 1999. Its headquarters are located at the Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University in Osaka, Japan. Currently PDBj supports a staff of 23 researchers and technicians who curate, edit, process, and distribute macromolecular structural data, collaborating with other members of wwPDB. In addition, PDBj researchers are active in a wide variety of bioinformatics projects: an XML-based description of protein structural data and associated query tools; eF-site, a database of electrostatic molecular surfaces of functional sites; PDBjViewer, a web-based viewer, which visualizes the molecular surface in addition to the conventional interactive molecular graphics facilities, parsing both the legacy PDB file and the PDB-XML file; ProMode, a database of molecular motions based on normal mode analysis; ASH, software and service for the multiple Alignment of Structural Homologues; PDB REMARK transcoder, a tool for extracting relevant information from PDB remark records; and eProtS, an encyclopedia of protein structures aimed at non-experts and students.

About the Institute for Protein Research, Osaka University:

Osaka University was founded in 1931 as the sixth national university in Japan. It started with two faculties, medicine and science, and now there are 10 faculties and schools, 12 graduate schools, 5 research institutes, and two university hospitals. The two campuses in Suita and Toyonaka cities occupy a total area of 1,429 million m2. There are about 4,500 teaching and administrative staff, and about 20,000 students. In faculties of medicine and science, extensive studies of protein science had been done, and the Institute for Protein Research was founded in 1958 to elucidate the life processes by multidisciplinary basic research of proteins, with cooperation from different fields such as physics, chemistry, biology and medicine. Due to requirements of research on peptides and X-ray crystallography, the institute established the first research center, Peptide Center, in 1962. This research center was converted several times, and finally the Research Center for Structural and Functional Proteomics was founded in 2002, composed of six laboratories, for the advancement of proteomics research.

Media contact: Joseph Blumberg
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Rutgers, the State University of New Jersey