Full Abstract No. 4
Authors: Kim Henrick1, Tom Oldfield2, Adel Golovin, John Tate, Sameer Velankar, Harry Boutselakis, Dimitris Dimitropoulos, Peter Keller, Eugene Krissinel, Phil McNeil, Jorge Pineda, Abdelkrim Rachedi, Antonio Suarez-Uruena, Jawahar Swaminathan, Mohamed Tagari
European Bioinformatics Institute, 1henrick@ebi.ac.uk 2oldfield@ebi.ac.uk
Title: MSD Relational Database, Search and Visualisation of Queries and Results
Representative figure/table:
Full abstract:
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 are aspects of our continious process of enhancing the quality and consistency of macromolecular structure data working towards the integration of various bioinformatics data resources. New simple form-based interfaces that allows users to query the MSD directly and the MSD atlas pages show all of the information in the MSD for a particular PDB entry. Additional search interfaces aimed at specific areas of interest, such as the environment of ligands and the secondary structures of proteins have been released. 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.
