The protein structure initiative structural genomics knowledgebase

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSI's high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communitie

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology

Protein Structure Initiative Publications, 2000-2016

These files contain the full list of the 2313 publications and book chapters written as part of the Protein Structure Initiative, from 2000-2016. This data was collected from PubMed and by manual entry by the PSI Structural Biology Knowledgebase's Publication Portal, managed by Wladek Minor at University of Virginia. These files were created at the end of the PSI project on June 30, 2017. The references are provided as lists in two formats: in CSV (comma-separated variables) format that can be read in Excel or other spreadsheet application, or an Endnote Library Import file (store-endnote-pubs). To import this library into Endnote, select File --> Import... and then under Options, select the Import Option "Endnote Library Import". Then this text file will be processed and loaded into the library. --created by the Structural Biology Knowledgebase, July 5, 2017. (sbkb.org

Sequence and structure comparison tool widget.

<p>The widget on the left is generated by the Javascript code on the right. Only the pointer (src) to the js file is required, the other lines allow the user to customize the look and feel of the widget to match their own Web page.</p

Semantic tagging.

<p>The box labeled usage shows how these tags are used in the html document. On the left is such a Web page (in italics) that has been semantically tagged. The Web page was created by David Goodsell as part of the RCSB PDB “Molecule of the Month” feature.</p