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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

Andersen Øivind et al., The conserved Phe GH5 of importance for hemoglobin intersubunit contact is mutated in gadoid fish Genome evolution and evolutionary systems biology. BMC Evolutionary Biology (2014) doi:10.1186/1471-2148-14-54

Thorsteinsson Kristina et al., Adherence to the cervical cancer screening program in women living with HIV in Denmark: comparison with the general population HIV and co-infections. BMC Infectious Diseases (2014) doi:10.1186/1471-2334-14-256

Pumirat Pornpan et al., The role of short-chain dehydrogenase/oxidoreductase, induced by salt stress, on host interaction of B. pseudomallei Microbe-host interactions and microbial pathogenicity. BMC Microbiology (2014) doi:10.1186/1471-2180-14-1

Dash Bhagirathi et al., Analysis of rare variations reveals roles of amino acid residues in the N-terminal extracellular domain of nicotinic acetylcholine receptor (nAChR) alpha6 subunit in the functional expression of human alpha6*-nAChRs. Molecular Brain (2014) doi:10.1186/1756-6606-7-35

Khafif Mehdi et al., Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes Results and data. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-222

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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