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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

Kaján László et al., FreeContact: fast and free software for protein contact prediction from residue co-evolution Sequence analysis (applications). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-85

Klementiev Boris et al., Anti-inflammatory properties of a novel peptide interleukin 1 receptor antagonist. Journal of Neuroinflammation (2014) doi:10.1186/1742-2094-11-27

Suresh Xavier M et al., Exploring the protein-protein interface of integrin-galectin complex for drug development against HIV infection- a bioinformatics study Abstracts from the 2nd International Science Symposium on HIV and Infectious Diseases (HIV SCIENCE 2014) 2nd International Science Symposium on HIV and Infectious Diseases (HIV SCIENCE 2014). BMC Infectious Diseases (2014) doi:10.1186/1471-2334-14-S3-P78

Vejayan Jaya et al., Comparative analysis of the venom proteome of four important Malaysian snake species Toxinology. Journal of Venomous Animals and Toxins including Tropical Diseases (2014) doi:10.1186/1678-9199-20-6

Teso Stefano et al., Joint probabilistic-logical refinement of multiple protein feature predictors Structural analysis. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-16

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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