E-MSD: an integrated data resource for bioinformatics

A Golovin, T J Oldfield, J G Tate, S Velankar, G J Barton, H Boutselakis, D Dimitropoulos, J Fillon, 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 SitnovS Sobhany, A Suarez-Uruena, G J Swaminathan, M Tagari, S Tromm, W Vranken, K Henrick

    Research output: Contribution to journalArticle

    66 Citations (Scopus)

    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/).

    Original languageEnglish
    Pages (from-to)D211-6
    JournalNucleic Acids Research
    Volume32
    Issue numberDatabase issue
    DOIs
    Publication statusPublished - 1 Jan 2004

    Keywords

    • Algorithms
    • Animals
    • Computational Biology
    • Databases, Protein
    • Humans
    • Internet
    • Ligands
    • Proteins
    • User-Computer Interface

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  • Cite this

    Golovin, A., Oldfield, T. J., Tate, J. G., Velankar, S., Barton, G. J., Boutselakis, H., Dimitropoulos, D., Fillon, J., Ionides, J. M. C., John, M., Keller, P. A., Krissinel, E., McNeil, P., Naim, A., Newman, R., Pajon, A., Pineda, J., Rachedi, A., Copeland, J., ... Henrick, K. (2004). E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Research, 32(Database issue), D211-6. https://doi.org/10.1093/nar/gkh078