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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

Schwarz Alexandra et al., Understanding the evolutionary structural variability and target specificity of tick salivary Kunitz peptides using next generation transcriptome data Genome evolution and evolutionary systems biology. BMC Evolutionary Biology (2014) doi:10.1186/1471-2148-14-4

Sakaguchi Masayoshi et al., Highly conserved salt bridge stabilizes a proteinase K subfamily enzyme, Aqualysin I, from Thermus aquaticus YT-1. AMB Express (2014) doi:10.1186/s13568-014-0059-2

Xu Yue-Juan et al., Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion Clinical-Molecular Genetics and Cytogenetics. BMC Medical Genetics (2014) doi:10.1186/1471-2350-15-78

Dhanjal Jaspreet Kaur et al., Structural insights into mode of actions of novel natural Mycobacterium protein tyrosine phosphatase B inhibitors Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics The Twelfth Asia Pacific Bioinformatics Conference (APBC 2014). BMC Genomics (2014) doi:10.1186/1471-2164-15-S1-S3

Rothan A Hussin et al., Identification of natural antimicrobial agents to treat dengue infection: In vitro analysis of latarcin peptide activity against dengue virus I don apos;t know (editor will assign section). BMC Microbiology (2014) doi:10.1186/1471-2180-14-140

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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