Protein Structure Initiative (PSI) Knowledgebase. We propose to create an Information repository and web portal called the Structural Biology Knowledgebase (SBKB), which will be an enhanced version of the current Structural Genomics Knowledgebase (SGKB). The SBKB will integrate the products of the PSI:Biology centers with data from external databases and community input to provide comprehensive sequence, structural, and functional information about all protein sequences In the structural genomics target tracking database, TargetDB, and the protein structure repository, the Protein Data Bank. In addition, we will continue to collaborate with the Nature Publishing Group to provide a "Gateway" to all information about structural biology and genomics. The SGKB has organized the products of the PSI efforts into seven modules (Experimental Data Tracking, Technology, Materials, Modeling, Annotation, Publications, and Metrics) so that all biological and biomedical researchers can access this information from a central "one-stop shop". In this proposal, we describe our plan to enhance the existing modules, and propose a new format to organize the underlying SBKB data into four categorical views: the Targets, Methods, Structure-Sequence-Function, and Models Hubs. This approach improves upon the current single-interface method by providing users with focused views of the information. We are also in the process of developing a data visualization tool that allows users to dynamically explore relationships in the SBKB data to enable the creation of new hypotheses. The SBKB will play an important role in the coordination of activities across the PSI:Biology Network and in outreach to diverse biological fields. Existing systems will be used to coordinate internal communications for PSI:Biology Network participants. In order to increase community involvement, we describe an recent enhancement to the community-nominated targets system, and propose a new web tool that collects community annotations for structures and targets and enables collaborations. Our goal is for the SBKB to become an engaging and widely-used resource for all biological and biomedical communities.

Public Health Relevance

The Structural Biology Knowledgebase will facilitate and simplify access to protein sequence, structure, and functional information for users from a variety of biological disciplines. In this way, it will be possible to gain both a broad and deep understanding of the molecular basis of biology and disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01GM093324-03
Application #
8303272
Study Section
Special Emphasis Panel (ZGM1-PPBC-5 (KB))
Program Officer
Preusch, Peter C
Project Start
2010-07-01
Project End
2015-06-30
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
3
Fiscal Year
2012
Total Cost
$2,364,622
Indirect Cost
$585,831
Name
Rutgers University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
001912864
City
New Brunswick
State
NJ
Country
United States
Zip Code
08901
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