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.|
- 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
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
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
Peng Qing et al., Isolation of a novel alkaline-stable lipase from a metagenomic library and its specific application for milkfat flavor production. Microbial Cell Factories (2014) doi:10.1186/1475-2859-13-1
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
Takeshita Daijiro et al., Structural basis of stereospecific reduction by quinuclidinone reductase. AMB Express (2014) doi:10.1186/2191-0855-4-6
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
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.
The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
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