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

Margaret J. Gabanyi, Paul D. Adams, Konstantin Arnold, Lorenza Bordoli, Lester G. Carter, Judith Flippen-Andersen, Lida Gifford, Juergen Haas, Andrei Kouranov, William A. McLaughlin, David I. Micallef, Wladek Minor, Raship Shah, Torsten Schwede, Yi Ping Tao, John D. Westbrook, Matthew Zimmerman, Helen M. Berman

Research output: Contribution to journalArticlepeer-review

48 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)45-54
Number of pages10
JournalJournal of Structural and Functional Genomics
Volume12
Issue number2
DOIs
StatePublished - Jul 2011

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Genetics

Keywords

  • Protein
  • Protein production
  • Structural biology
  • Structural databases
  • Structural genomics
  • Theoretical models

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