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Data Deposition and Annotation at the Worldwide Protein Data Bank

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Abstract

The Protein Data Bank (PDB) is the repository for three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive is free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and general audiences to understand biological phenomenon at a molecular level. Analysis of this structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

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Acknowledgment

The authors would like to acknowledge the staff of the 3 wwPDB sites, and our advisory committees. At the RCSB PDB, we acknowledge the programing staff consisting of Li Chen, Zukang Feng, Vladimir Guranovic, Andrei Kouranov, John Westbrook, Huanwang Yang; and the annotation staff consisting of Jaroslaw Blaszczyk, Batsal Devkota, Guanghua Gao, Sutapa Ghosh, Irina Persikova, Bohdan Schneider, Monica Sekharan, Chenghua Shao, Lihua Tan, and Jing Zhou. At PDBe, we acknowledge annotators, Richard Newman, Gaurav Sahni, Glen van Ginkel, and Sanchayita Sen. At PDBj, we acknowledge annotators Minyu Chen, Mayumi Inoue, Reiko Igarashi, Yumiko Kengaku, and Kanna Matsuura. The RCSB PDB is operated by Rutgers, The State University of New Jersey and the San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego. It is supported by funds from the National Science Foundation, the National Institute of General Medical Sciences, the Office of Science, Department of Energy, the National Library of Medicine, the National Cancer Institute, the National Center for Research Resources, the National Institute of Biomedical Imaging and Bioengineering, the National Institute of Neurological Disorders and Stroke, and the National Institute of Diabetes and Digestive and Kidney Diseases. PDBe is supported by funds from the Wellcome Trust (GR062025MA), 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 European Molecular Biology Laboratory. PDBj is supported by grant-in-aid from the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency (BIRD-JST), and the Ministry of Education, Culture, Sports, Science, and Technology (MEXT). The BMRB is supported by NIH grant LM05799 from the National Library of Medicine.

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  1. Kyle Burkhardt

    Present address: Office of Research and Project Administration, Princeton University, 4 New South Building, Princeton, NJ, 08544, USA

Authors and Affiliations

  1. Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA

    Shuchismita Dutta, Kyle Burkhardt, Jasmine Young & Helen M. Berman

  2. The Macromolecular Structure Database at the European Bioinformatics Institute PDB-e, EMBL Outstation-Hinxton, Cambridge, CB10 1SD, UK

    Ganesh J. Swaminathan & Kim Henrick

  3. Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Takanori Matsuura & Haruki Nakamura

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  1. Shuchismita Dutta
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Correspondence to Helen M. Berman.

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Shuchismita Dutta, Kyle Burkhardt, and Ganesh J. Swaminathan have contributed equally to this work.

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Dutta, S., Burkhardt, K., Young, J. et al. Data Deposition and Annotation at the Worldwide Protein Data Bank. Mol Biotechnol 42, 1–13 (2009). https://doi.org/10.1007/s12033-008-9127-7

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