MSDsite: A database search and retrieval system for the analysis and viewing of bound ligands and active sites

Authors

  • Adel Golovin,

    1. EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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  • Dimitris Dimitropoulos,

    1. EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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  • Tom Oldfield,

    1. EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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  • Abdelkrim Rachedi,

    1. EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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  • Kim Henrick

    Corresponding author
    1. EMBL Outstation, The European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    • EMBL Outstation, the European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UK
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Abstract

The three-dimensional environments of ligand binding sites have been derived from the parsing and loading of the PDB entries into a relational database. For each bound molecule the biological assembly of the quaternary structure has been used to determine all contact residues and a fast interactive search and retrieval system has been developed. Prosite pattern and short sequence search options are available together with a novel graphical query generator for inter-residue contacts. The database and its query interface are accessible from the Internet through a web server located at: http://www.ebi.ac.uk/msd-srv/msdsite. Proteins 2005. © 2004 Wiley-Liss, Inc.

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