The Data and Dissemination Core [Babbitt (UCSF) and Buriey (Lilly), CoDirectors] addresses the requirements for data gathering/coordination, information dissemination, and bioinformatics as specified in the RFA for U54 Centers. This Core combines Cores B (Information Dissemination and Data-Coordinating Core) and C (Bioinformatics). For the Enzyme Function Initiative (EFI), the Data and Dissemination Core will be implemented and managed using four primary resources working together to ensure ease of data input and tracking by EFI members, coordination of experimental and computational data, implementation and access to analysis and visualization tools, and dissemination of data and information to EFI investigators and the public. Instructions for depositing data and information to the EFI and for using the tools and results of EFI efforts will be provided in the form of help files and online tutorials. Strategies and protocols for dissemination of EFI resources and materials, software and experimental results will also be provided by the core resources. Each is listed briefly below and described in detail in the sections following. EFI results will also be disseminated through publications in the peer-reviewed literature, presentations by EFI investigators at meetings and other venues, and through workshops developed for presentation at meetings of scientific societies and other appropriate organizations. 1. The EFI Website, the responsibility of the Administrative Core at UIUC (Gerit, Director), will be the official site for the EFI, providing information about the project and resources and acting as one of the portals for access to its data, results and materials. The homepage will provide tutorials, listings of publications, news, and other relevant information. Links will enable access to the Data Resource (Laboratory Information Management System for EFI members), the Structure Function Linkage Database, and the Computation Core (see sections 2-4 below). 2. The Data Resource (Sauder, Director) will rely on a state-of-the-art Laboratory Information Management System (LIMS) that has been optimized for high-throughput structural biology and studies of protein ligand-interactions. EFI experimental results and methods will be stored in the Data Resource for transfer to appropriate databases for dissemination. Target status will be automatically shared with the Structure Function Linkage Database (SFLD), together with other associated data. Structure and function results will be available through public websites linked to the Data Resource and through the other primary resources, including the EFI website and the SFLD. Because the core architecture of LIMS has already been implemented and its efficacy validated by a large numbers of users, this resource can provide extensive functionality at minimal cost to the EFI, with the requested funds used to extend LIMS to accommodate the specialized needs of the EFI and to integrate it with the other EFI resources described in this proposal. 3. The Structure Function Linkage Database (SFLD) (Babbitt, Director) will provide access to information about the superfamilies targeted by the Bridging Projects hierarchically classified by both sequence/structural and functional similarity into superfamilies and [monofunctional] families. Developed originally to analyze structure-function relationships of functionally diverse enzyme superfamilies, the SFLD will enable user access to EFI data and results in two major ways. First, the SFLD will serve as a continually updated archive of all sequences, structures (obtained experimentally or from models), and functions that are known for Bridging Project superfamilies, including functions discovered by the EFI Bridging Projects and Scientific Cores. Second, the SFLD will provide the results of computational (bioinformatic) and experimental analyses of these superfamilies in the context of their structure-function relationships to EFI investigators and the public. An extensive set of browse and search tools provide access to these data and information. Because the core architecture of the SFLD has already been implemented, EFI funds can be used principally to create new analysis and visualization functionality and to implement integration and sharing of data and information with the other dissemination resources. Computational analysis of superfamily structure-function relationships for target identification and function prediction is described in the Superfamily/Genome Core. 4. The Computation Core (Jacobson, Director) will create or extend existing resources to disseminate modeling and docking results along with relevant protocols and methods. As deemed useful, subsets of the raw data will be available for dissemination by LIMS or the SFLD and via links from the EFI Website. Because data and results are still closely tied to the further development of research methods, data coordination and bioinformatics for the Computation Core is described in that section rather than here. Only the dissemination and outreach efforts for the Computation Core are described in this Core proposal.

Agency
National Institute of Health (NIH)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54GM093342-05
Application #
8665975
Study Section
Special Emphasis Panel (ZGM1)
Project Start
Project End
Budget Start
Budget End
Support Year
5
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
DUNS #
City
Champaign
State
IL
Country
United States
Zip Code
61820
Mashiyama, Susan T; Malabanan, M Merced; Akiva, Eyal et al. (2014) Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol 12:e1001843
Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E et al. (2014) The Structure-Function Linkage Database. Nucleic Acids Res 42:D521-30
Zheng, Heping; Hou, Jing; Zimmerman, Matthew D et al. (2014) The future of crystallography in drug discovery. Expert Opin Drug Discov 9:125-37
Wichelecki, Daniel J; Graff, Dylan C; Al-Obaidi, Nawar et al. (2014) Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily. Biochemistry 53:4087-9
Dong, Guang Qiang; Calhoun, Sara; Fan, Hao et al. (2014) Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model 54:1687-99
Wichelecki, Daniel J; Vendiola, Jean Alyxa Ferolin; Jones, Amy M et al. (2014) Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate. Biochemistry 53:5692-9
Bouvier, Jason T; Groninger-Poe, Fiona P; Vetting, Matthew et al. (2014) Galactaro ?-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily. Biochemistry 53:614-6
Wichelecki, Daniel J; Froese, D Sean; Kopec, Jolanta et al. (2014) Enzymatic and structural characterization of rTS? provides insights into the function of rTS?. Biochemistry 53:2732-8
Pandya, Chetanya; Dunaway-Mariano, Debra; Xia, Yu et al. (2014) Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily. Proteins 82:1896-906
Kumar, Ritesh; Zhao, Suwen; Vetting, Matthew W et al. (2014) Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine. MBio 5:e00933-13

Showing the most recent 10 out of 49 publications