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
Mótyán András János et al., A molecular model of the full-length human NOD-like receptor family CARD domain containing 5 (NLRC5) protein Structural analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-275
Lopez Daniel et al., Concomitant prediction of function and fold at the domain level with GO-based profiles Selected proceedings from the Automated Function Prediction Meeting 2011 Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-S3-S12
Zheng Wei Hao et al., Evolutionary relationships of ATP-Binding Cassette (ABC) uptake porters Microbial biochemistry, physiology and metabolism. BMC Microbiology (2013) doi:10.1186/1471-2180-13-98
Yaseen Ashraf et al., Dinosolve: a protein disulfide bonding prediction server using context-based features to enhance prediction accuracy Selected articles from the 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012) The 9th Annual Biotechnology and Bioinformatics Symposium (BIOT 2012). BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-S13-S9
Yaghmaei Sepideh et al., Agonist and antagonist binding to the nuclear vitamin D receptor: dynamics, mutation effects and functional implications. In Silico Pharmacology (2013) doi:10.1186/2193-9616-1-2
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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