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The Protein Structure Initiative Structural Biology Knowledgebase

Tutorial and training materials by OpenHelix

Learn to use the PSI-Nature Structural Biology Knowledgebase (SBKB), which integrates a wide variety of structural biology and structural genomics resources into one easy to navigate site in order to turn this vast set of information into knowledge important in understanding living systems and disease. Each month the Structural Biology Update provides: editorials on research advances, a primer on a featured molecule, news articles, new additions to the SBKB research library, and a listing of events for the structural biology and structural genomics community. The SBKB connects biological information from a wide variety of popular web resources (KEGG, Reactome, NCBI, and more) with vast amounts of structural information available from the Protein Data Bank (PDB) and other Protein Structure Initiative (PSI) resources into one knowledgebase. Its simple search interface allows researchers to search by sequence, structure or text and provides well organized, easy to navigate result summaries and detailed reports of results.
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You'll learn:

  • To search the SBKB with a sequence or structure, and how to navigate the results
  • How to navigate search results to obtain information from various information sources
  • How text searches differ from other types of SBKB searches, and what information is available in their results
  • How you can propose biologically relevant proteins as structural targets to the Protein Structure Initiative
  • About other valuable features of the SBKB resource


Related tutorials

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

DePietro J Paul et al., Quantification of the impact of PSI:Biology according to the annotations of the determined structures Computational analysis. BMC Structural Biology (2013) doi:10.1186/1472-6807-13-24

Fajardo J Eduardo et al., Protein structure based prediction of catalytic residues Structural analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-63

Lee David et al., 1,000 structures and more from the MCSG. BMC Structural Biology (2011) doi:10.1186/1472-6807-11-2

Hodis Eran et al., Proteopedia - a scientific "wiki" bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biology (2008) doi:10.1186/gb-2008-9-8-r121

More about the resource:

PSI-Nature Structural Biology Knowledgebase (SBKB), formerly known as the Structural Genomics Knowledgebase (SGKB), is brought to you by the Nature Publishing Group (NPG) and Protein Structure Initiative (PSI), which is an effort supported by the National Institutes of Health with the goal of dramatically reducing the costs and time required to determine three-dimensional protein structures. The PSI actively encourages the broad scientific community to participate in the selection of proteins for structure determination. PSI has created the PSI-Nature Structural Biology Knowledgebase as a means of increasing its outreach, accessibility, and impact on biomedical research. The PSI-Nature Structural Biology Knowledgebase is updated on a monthly basis.


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