E-MSD: an integrated data resource for bioinformatics - PubMed (original) (raw)
. 2004 Jan 1;32(Database issue):D211-6.
doi: 10.1093/nar/gkh078.
T J Oldfield, J G Tate, S Velankar, G J Barton, H Boutselakis, D Dimitropoulos, J Fillon, A Hussain, J M C Ionides, M John, P A Keller, E Krissinel, P McNeil, A Naim, R Newman, A Pajon, J Pineda, A Rachedi, J Copeland, A Sitnov, S Sobhany, A Suarez-Uruena, G J Swaminathan, M Tagari, S Tromm, W Vranken, K Henrick
Affiliations
- PMID: 14681397
- PMCID: PMC308812
- DOI: 10.1093/nar/gkh078
E-MSD: an integrated data resource for bioinformatics
A Golovin et al. Nucleic Acids Res. 2004.
Abstract
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/).
Figures
Figure 1
(a) The MSDlite query form. The form is divided into three panels. The two left-hand panels show search fields, with the most commonly used terms found in the uppermost panel. The right-hand panel allows the user to configure the results that will be returned by their query. (b) A sample MSDlite results page. Results are presented in a simple table, divided across several pages if necessary. Result items are hyperlinked to additional resources wherever possible. For every search hit, the PDB accession code is linked to the MSD atlas page for that entry, and the ‘View’ link allows the user to visualize the structure using AstexViewer@MSD-EBI.
Figure 1
(a) The MSDlite query form. The form is divided into three panels. The two left-hand panels show search fields, with the most commonly used terms found in the uppermost panel. The right-hand panel allows the user to configure the results that will be returned by their query. (b) A sample MSDlite results page. Results are presented in a simple table, divided across several pages if necessary. Result items are hyperlinked to additional resources wherever possible. For every search hit, the PDB accession code is linked to the MSD atlas page for that entry, and the ‘View’ link allows the user to visualize the structure using AstexViewer@MSD-EBI.
Figure 2
The MSD atlas page for PDB entry 1hdk. The atlas pages present all available information for a particular PDB entry. Related information is grouped into separate tab panes, covering sequence, ligand data, journal citations, etc. Information in the atlas pages is hyperlinked wherever possible, directing the user to related MSD and external resources.
Figure 3
(a) The results of an MSDsite query. The results pages show the residues that interact with a given ligand, including the classification of each interaction and geometrical information in the case of metal coordination interactions. (b) The MSDsite statistics for a ligand binding environment. The environment is described in a simple chart, showing the most commonly found residues in the environment for a given ligand. Residues may be classified according to the type of secondary structure element in which they are found. Statistics can also be obtained for a complete ligand binding environment.
Figure 3
(a) The results of an MSDsite query. The results pages show the residues that interact with a given ligand, including the classification of each interaction and geometrical information in the case of metal coordination interactions. (b) The MSDsite statistics for a ligand binding environment. The environment is described in a simple chart, showing the most commonly found residues in the environment for a given ligand. Residues may be classified according to the type of secondary structure element in which they are found. Statistics can also be obtained for a complete ligand binding environment.
Figure 4
The MSDpro query interface. MSDpro allows the user to describe complex queries by dragging-and-dropping search and result terms from the lists on the left of the interface into the corresponding panels on the right. Search terms can be combined and using logical operations AND, OR and NOT. Results of a query are presented as a simple table within the interface itself, or they can be viewed through the MSDlite result pages.
Figure 5
AstexViewer@MSD-EBI allows the user to view multiple, superposed structures and aligned sequences. The viewer provides a lightweight, easy-to-use interface for visualizing the results of various MSD searches.
References
- Berman H.M., Battistuz,T., Bhat,T.N., Bluhm,W.F., Bourne,P.E., Burkhardt,K., Feng,Z., Gilliland,G.L., Iype,L., Jain,S. et al. (2002) The Protein Data Bank. Acta Crystallogr. D, 58, 899–907. - PubMed
- Orengo C.A., Pearl,F.M. and Thornton,J.M. (2003) The CATH domain structure database. Methods Biochem. Anal., 44, 249–271. - PubMed