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Data Deposition and Annotation at the Worldwide Protein Data Bank

  • Protocol
Structural Proteomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 426))

 

The Protein Data Bank (PDB) is the repository for the three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive are 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 lay audiences to understand biological phenomena at a molecular level. Analysis of these 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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Acknowledgments

The authors acknowledge the staff of all wwPDB sites, and our advisory committees.

At the RCSB PDB, we acknowledge the programming staff consisting of Li Chen, Zukang Feng, Vladimir Guranovic, Andrei Kouranov, John Westbrook, Huanwang Yang; and the annotation staff consisting of Jaroslaw Blaszczyk, Guanghua Gao, Irina Persikova, Massy Rajabzadeh, Bohdan Schneider, Monica Sekharan, Monica Sundd, Jasmine Young, and Muhammed Yousufuddin.

At MSD-EBI, we acknowledge annotators Adamandia Kapopoulou, Richard Newman, Gaurav Sahni, Glen van Ginkel, Sanchayita Sen, and Sameer Velankar.

At PDBj, we acknowledge annotators Reiko Igarashi, Yumiko Kengaku, Kanna Matsuura and Yasuyo Morita.

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.

EBI-MSD 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 Techno

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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, Piscataway, New Jersey

    Shuchismita Dutta, Kyle Burkhardt & Helen M. Berman

  2. The Macromolecular Structure Database at the European Bioinformatics Institute MSD-EBI, EMBL Outstation-Hinxton, Cambridge, UK

    Ganesh J. Swaminathan & Kim Henrick

  3. Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka, Japan

    Takashi Kosada & Haruki Nakamura

Authors
  1. Shuchismita Dutta
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  2. Kyle Burkhardt
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  3. Ganesh J. Swaminathan
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  5. Kim Henrick
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  6. Haruki Nakamura
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Editor information

Editors and Affiliations

  1. School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland, Australia

    Bostjan Kobe

  2. School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia

    Mitchell Guss

  3. School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia

    Thomas Huber

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Dutta, S. et al. (2008). Data Deposition and Annotation at the Worldwide Protein Data Bank. In: Kobe, B., Guss, M., Huber, T. (eds) Structural Proteomics. Methods in Molecular Biology™, vol 426. Humana Press. https://doi.org/10.1007/978-1-60327-058-8_5

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  • DOI: https://doi.org/10.1007/978-1-60327-058-8_5

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-809-6

  • Online ISBN: 978-1-60327-058-8

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