ABSTRACT
The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.
Subject(s)
Databases, Protein , Microscopy, Electron , Nuclear Magnetic Resonance, Biomolecular , Proteins/chemistry , Proteins/ultrastructure , Computational Biology , Databases, Protein/standards , Europe , Internet , Macromolecular Substances/chemistry , Reproducibility of Results , User-Computer InterfaceABSTRACT
The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the Protein Data Bank (PDB) and to work towards the integration of various bioinformatics data resources. We have implemented a simple form-based interface that allows users to query the MSD directly. The MSD 'atlas pages' show all of the information in the MSD for a particular PDB entry. The group has designed new search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins. We have also implemented a novel search interface that begins to integrate separate MSD search services in a single graphical tool. We have worked closely with collaborators to build a new visualization tool that can present both structure and sequence data in a unified interface, and this data viewer is now used throughout the MSD services for the visualization and presentation of search results. Examples showcasing the functionality and power of these tools are available from tutorial webpages (http://www. ebi.ac.uk/msd-srv/docs/roadshow_tutorial/).
Subject(s)
Computational Biology , Databases, Protein , Proteins/chemistry , Proteins/metabolism , Algorithms , Animals , Humans , Internet , Ligands , User-Computer InterfaceABSTRACT
This paper describes the design and implementation of a Web-based deposition system, EMDep, for macro-molecular volumes determined by electron microscopy and deposited at the European Bioinformatics Institute (EBI) for inclusion in the Electron Microscopy Data Base (EMDB). EMDep is a flexible and portable system (http://www.ebi.ac.uk/msd-srv/emdep/) that allows for the acceptance and validation of data, by an interactive depositor-driven operation. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators, for the complete and accurate description of the structural experiment and its results.
Subject(s)
Image Processing, Computer-Assisted/methods , Internet , Microscopy, Electron/methods , Algorithms , Databases as Topic , SoftwareABSTRACT
The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.
