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.
You will learn:
This tutorial is a part of the tutorial group Protein-centric and protein structure resources. You might find the other tutorials in the group interesting:
Pfam: Protein Domain families
UniProt: UniProt, Universal Protein Resource
MMDB: Molecular Modeling Database at NCBI
Entrez Protein: NCBI's Entrez Protein for amino acid-centric information
Structural Biology Knowledgebase: The Protein Structure Initiative Structural Biology Knowledgebase
Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.
Video Tip of the Week: Designing proteins, using Rosetta: As often happens, last week's tip on visualizing structures led me to some more reading and thinking about creating protein structures. And although it's important for biologists to be able to use more...
Video Tip of the Week: Aquaria, streamlined access to protein structures for biologists: This week's Video Tip of the Week is Aquaria, a new resource for exploring protein structures, mutations, and similarities to other proteins. It's a very well-designed and interactive experience for en...
What's The Answer? (mobile bioinformatics apps): Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at Biostars that...
Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...
Video Tip of the Week: The PSI SBKB's New Content Hubs: In today's tip I will feature the newly organized content hubs over at the Protein Structure Initiative's Structural Biology Knowledgebase, or PSI SBKB. We do have a free, full-length tutorial on the ...
Recent BioMed Central research articles citing this resource
Dresch Philipp et al., Fungal strain matters: colony growth and bioactivity of the European medicinal polypores Fomes fomentarius, Fomitopsis pinicola and Piptoporus betulinus. AMB Express (2015) doi:10.1186/s13568-014-0093-0
Wang Caihua et al., Predicting target-ligand interactions using protein ligand-binding site and ligand substructures Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Systems Biology The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Systems Biology (2015) doi:10.1186/1752-0509-9-S1-S2
Son Minky et al., Structural importance of the C-terminal region in pig aldo-keto reductase family 1 member C1 and their effects on enzymatic activity. BMC Structural Biology (2015) doi:10.1186/s12900-014-0028-7
Lauber Jennifer et al., Expression of the functional recombinant human glycosyltransferase GalNAcT2 in Escherichia coli. Microbial Cell Factories (2015) doi:10.1186/s12934-014-0186-0
Vasylenko Tamara et al., SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Bioinformatics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Bioinformatics (2015) doi:10.1186/1471-2105-16-S1-S8