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RCSB Protein Data Bank

Tutorial and training materials by OpenHelix

Learn to use the RCSB Protein Data Bank, or PDB, a tremendous resource that provides a variety of tools and resources for accessing data in the PDB archive. The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB not only provides tools for access PDB archive data but they also curate and annotate PDB data. Researchers can access images of structures, as well as detailed experimental data. Links to other important details such as family and domain information, ligand details, pathway data, and more, can also be found. Many tools to examine and manipulate the three-dimensional structures are available. The RCSB PDB also provides extensive educational resources, including a molecule of the month feature and other materials that can be used to understand the basics of structural biology.
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You'll learn:

  • how to search for structures and related information using a variety of strategies
  • to understand the results and structure summary pages and link to additional information
  • how to visualize and manipulate the structures
  • to customize your results by using the many formatting options


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This tutorial is a part of the tutorial group PDB/SBKB. You might find the other tutorials in the group interesting:

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Recent BioMed Central research articles citing this resource

Wen Jingran et al., Structure prediction of polyglutamine disease proteins: comparison of methods Selected articles from the 10th Annual Biotechnology and Bioinformatics Symposium (BIOT 2013) The 10th Annual Biotechnology and Bioinformatics Symposium (BIOT 2013). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-S7-S11

Khan Kasib Muhammad et al., Identification of two novel HSP90 proteins in Babesia orientalis : molecular characterization, and computational analyses of their structure, function, antigenicity and inhibitor interaction. Parasites Vectors (2014) doi:10.1186/1756-3305-7-293

Swuec Paolo et al., Molecular mechanism of double Holliday junction dissolution. Cell Bioscience (2014) doi:10.1186/2045-3701-4-36

Ranjan Aashish et al., Functional analysis of COP1 and SPA orthologs from Physcomitrella and rice during photomorphogenesis of transgenic Arabidopsis reveals distinct evolutionary conservation Plant-abiotic interactions. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-178

Fukunaga Tsukasa et al., CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biology (2014) doi:10.1186/gb-2014-15-1-r16

More about the resource:

The Protein Data Bank (PDB) archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the Worldwide PDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB develops resources to perform simple and advanced searches based on annotations relating to sequence, structure and function, and to visualize, download, and analyze molecules. The RCSB PDB also supports an educational view of PDB data, called PDB-101.


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