PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
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id="title" class="nomar"PSI Structural Biology Knowledgebase

The PSI Structural Biology Knowledgebase is one of two PSI:Biology Resource Centers.  Comprised of 6 consortia groups, we facilitate public access to the results of the entire Protein Structure Initiative on the web, and integrate them with information from the greater biological community.

Member Institutions

  • Rutgers, The State University of New Jersey
  • University of Basel and BioZentrum
  • Lawrence Berkeley National Labortory
  • The Commonwealth Medical College
  • University of Virginia School of Medicine
  • University of California, Irvine

 

Contact Information

Helen M. Berman

berman@rcsb.rutgers.edu

Margaret Gabanyi

gabanyi@rcsb.rutgers.edu

General information

comments@sbkb.org

 

Research Description:

PSI: Biology consists of a network of research laboratories whose goal it is to use high throughput structural biology to understand the functions of biological macromolecules. The PSI Structural Biology Knowledgebase facilitates public access to the results of these efforts and integrates them with information from other biological resources.

To accomplish this, we create a centralized web portal (http://sbkb.org) that allows access to the status and annotations from 100 different sources for PSI targets. When available, the experimental structures or homology models are provided for any UniProt sequence. Extended data is organized by our partner portals:

  • Main SBKB portal: research highlights, protein query services, and PSI information.
  • TargetTrack: an experiments deposition and tracking database.
  • Protein Model Portal: a theoretical models search portal.
  • PSI Annotations: two tools, KB-Rank and KB-Role to explore and predict structure-function relationships.
  • PSI Technology Portal: a catalog of PSI-developed technologies
  • PSI Publications Portal: a list of all PSI-supported publications and altmetrics.
  • MPStruc: The “Membrane Proteins of Known 3D Structure” website.
  • BioSync: The “Structural Biologist's Guide to High Energy Data Collection Facilities” website.

We also provide the facilities for such data capture, maintain an outreach program for the PSI:Biology Network such as the Community-Nomination Portal, and manage a secure internal communication portal for PSI investigators.

 

Key Publications

1. Gabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R,Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM. The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics. 2011 Jul;12(2):45-54. [doi: 10.1007/s10969-011-9106-2]. PMID: 21472436

2. Arnold K, Kiefer F, Kopp J, Battey JN, Podvinec M, Westbrook JD, Berman HM, Bordoli L, Schwede T. (2009) The Protein Model Portal. J Struct Funct Genomics. 2009 Mar;10(1):1-8. [doi:10.1007/s10969-008-9048-5]

3. Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. J Struct Funct Genomics. 2012 Jun;13(2):57-62. [doi:10.1007/s10969-012-9133-7]

4. Julfayev ES, McLaughlin RJ, Tao YP, McLaughlin WA. KB-Rank: efficient protein structure and functional annotation identification via text query. J Struct Funct Genomics. 2012 Jun;13(2):101-10. [doi: 10.1007/s10969-012-9125-7]

 

Related Websites

Main SBKB Portal: http://sbkb.org

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health