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 ofthe 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 willcontinue 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 ofthe 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 ofthe 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 PSLBiology 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.
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.
|Grabowski, Marek; Niedzialkowska, Ewa; Zimmerman, Matthew D et al. (2016) The impact of structural genomics: the first quindecennial. J Struct Funct Genomics 17:1-16|
|Gabanyi, Margaret J; Berman, Helen M (2015) Protein structure annotation resources. Methods Mol Biol 1261:3-20|
|Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R et al. (2015) Data to knowledge: how to get meaning from your result. IUCrJ 2:45-58|
|Schmidt, Tobias; Bergner, Andreas; Schwede, Torsten (2014) Modelling three-dimensional protein structures for applications in drug design. Drug Discov Today 19:890-7|
|Monastyrskyy, Bohdan; Kryshtafovych, Andriy; Moult, John et al. (2014) Assessment of protein disorder region predictions in CASP10. Proteins 82 Suppl 2:127-37|
|Gallo Cassarino, Tiziano; Bordoli, Lorenza; Schwede, Torsten (2014) Assessment of ligand binding site predictions in CASP10. Proteins 82 Suppl 2:154-63|
|DePietro, Paul J; Julfayev, Elchin S; McLaughlin, William A (2013) Quantification of the impact of PSI:Biology according to the annotations of the determined structures. BMC Struct Biol 13:24|
|Haas, Juergen; Roth, Steven; Arnold, Konstantin et al. (2013) The Protein Model Portal--a comprehensive resource for protein structure and model information. Database (Oxford) 2013:bat031|
|Schwede, Torsten (2013) Protein modeling: what happened to the "protein structure gap"? Structure 21:1531-40|
|Julfayev, Elchin S; McLaughlin, Ryan J; Tao, Yi-Ping et al. (2012) KB-Rank: efficient protein structure and functional annotation identification via text query. J Struct Funct Genomics 13:101-10|
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