Guide for the EFI-Database (EFI-DB)

Transcription

1 Guide for the EFI-Database (EFI-DB) Use this guide to become familiar with the information available in the EFI experimental database, the EFI-DB. Helpful annotations are in yellow. 10/2011

2 About the EFI-DB 1 What is the EFI-DB? The EFI-DB serves as the EFI s public database of experimental data. The database stores details of all cloning, purification, and structure determination experiments, as well as the results of in vivo and in vitro analyses as they become publicly available. The information is presented in a dynamic, interactive format to allow one to quickly browse through all experimental data. The EFI-DB database contains a subset of the information stored in its companion database, the LabDB LIMS (Laboratory Information Management System). LabDB is used internally by the EFI staff to record vast amounts of data describing the experiments conducted in the center; in many cases LabDB interfaces directly with the equipment used by EFI. What is the EFI-DB used for? To locate EFI targets and track their experimental status. The experimental ( wet ) data for each target in EFI is also linked to a corresponding page in the Structure-Function Linkage Database (SFLD) with the bioinformatics ( dry ) data for that target. EFI-DB also provides data to other public databases, such as TargetDB, PepCDB, and the Protein Data Bank. How can I use the EFI-DB? - Browse and search the list of EFI targets - Display experimental track of any EFI target - Check if a protein of interest has a homologue among the EFI targets - View X-ray crystallography structures determined and annotated by EFI members - Download and view interactive structure descriptions, using ICM viewer technology from Molsoft LLC - See overall progress and statistics of the EFI project Who maintains EFI-DB? EFI-DB and LabDB are developed and maintained on the behalf of the Enzyme Function Initiative by the group of Prof. Wladek Minor at the University of Virginia. Contact: labdb@enzymefunction.org

3 Getting Started Web Page: EFI-DB Home 2 Website links are in red. EFI-DB menu EFI main website menu About News Use Guides Contact

4 Search EFI Targets Web Page: Homologue Search 3 Select data set, E value and provide sequence

5 Browse EFI Targets Web Page: Targets 4 Select menu items to reformat table below to display specific superfamily targets. Select to reformat table below: - Filter Targets by organism, species, keyword, stage, or lab - Jump to Target via EFI-DB, GI number, or locus tag - Filter Columns to display EFI-ID, superfamily, GI, locus tag, organism, gene name, description, length, homologue PDB, homologue PDB % identity, stage

6 Browse EFI Targets, cont. Web Page: Targets 5 Click EFI-ID to view individual target page Click GI to go to NCBI protein page Click organism to go to NCBI taxonomy page Click SFLD to view informatics page EFI Superfamily NCBI Description Selection Most Advanced Rationale Experimental Stage

7 Download EFI Data Web Page: Targets 6 Click to download EFI data for the targets represented in the table below.

8 EFI Target Information Web Page: Specific Target View (example) 7 Experimental tree where each box represents an experiment. Dark boxes lead to the most advanced stage. Click SFLD to view Informatics page General target information

9 EFI Target Information, cont. Web Page: Specific Target View (example) 8

10 EFI Structures Web Page: Structures 9 Click title to view individual structure page 9 Structures Click to go to external databases

11 EFI Structures, cont. Web Page: Specific Deposit View (example) 10 Click to go to view experimental tree 9 Structures crystallization details

12 EFI Structures, cont. Web Page: Electronic Structure Description 11 Click to view interactive structure visualizations (requires Molsoft download) 9 Structures Interactive poses

13 Progress Web Page: Progress 12 Select to reformat table and chart below by superfamily, organism, or species

14 Statistics Web Page: Statistics 13 Select to reformat table and chart below by superfamily, organism, or species Select menu items to view superfamilyspecific and structure pipeline statistics

15 Data Sharing Plan 14 1) Gathering and grouping of sequence similarity networks and other approaches for phylogenetics by the Superfamily/Genome Core Deposited in the SFLD database and will be available immediately (prior to publication) to the scientific community. 2) Purified proteins produced by the Protein Core The identities and progress of proteins in the pipeline will be available immediately (prior to publication) to the scientific community via the TargetDB and PepCDB databases. The purified proteins will be available only to the members of the EFI; the clones for the proteins will be available to the scientific community via the PSI-MR. 3) Three dimensional structures of target proteins by x ray crystallography in the Structure Core The structures determined by the structure core will be deposited immediately (prior to publication) in the PDB. This plan parallels that used by the NIGMS PSI-2 large scale centers for structure deposition. 4) Three dimensional structures of target proteins by homology modeling, in silico docking poses of virtual libraries of metabolites and high energy intermediates, and the resulting rank-ordered hit lists of predicted substrates by the Computation Core. The homology models and hit lists will be immediately available to all members of the EFI, but will not be made available to the scientific community until functional assignments and/or improvements in computational algorithms based on these results have been published. The computation core will provide web-based portals to enable the community to use the software for homology modeling, docking, and related tasks. All of the underlying software is freely available to non-profit institutions, and new software developed by the EFI will be open-source. 5) Focused libraries of ligands and substrates by the Bridging Projects The identities of these libraries will be provided on the EFI website; samples will be made available on request as quantities permit. The procedures for their syntheses will be provided via the EFI website; clones for any EFI-specific proteins required for library synthesis will be available from the PSI MR. 6) Results of library screening and detailed kinetic analyses by the Bridging Projects The results of focus library screening and detailed kinetic analyses will be immediately available to all members of the EFI, but will not be made available to the scientific community until functional assignments and/or improvements in computational algorithms based on these results have been published. 7) Results of phenotypic and metabolomic analyses by the Microbiology Core The results of phenotypic and metabolomic analyses will be immediately available to all members of the EFI, but will not be made available to the scientific community until functional assignments and/or improvements in computational algorithms based on these results have been published.