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:

  • 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
TUTORIAL RELATED CONTENT

TUTORIALS

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

CATEGORIES

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.

BLOG POSTS

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 ...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Cortes-Ciriano Isidro et al., Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling Graphical Abstract. Journal of Cheminformatics (2015) doi:10.1186/s13321-014-0049-z

Li Guangdi et al., A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biology Direct (2015) doi:10.1186/s13062-014-0031-8

Tahoun Amin et al., Functional analysis of bovine TLR5 and association with IgA responses of cattle following systemic immunisation with H7 flagella. Veterinary Research (2015) doi:10.1186/s13567-014-0135-2

Ohkouchi Naohiko et al., Biochemical and physiological bases for the use of carbon and nitrogen isotopes in environmental and ecological studies Biogeosciences. Progress in Earth and Planetary Science (2015) doi:10.1186/s40645-015-0032-y

El Frihmat Yassine et al., Reconstruction of productivity signal and deep-water conditions in Moroccan Atlantic margin (~35°N) from the last glacial to the Holocene Earth and Environmental Sciences. SpringerPlus (2015) doi:10.1186/s40064-015-0853-6