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Related Experiment Videos

PDBSprotEC: a Web-accessible database linking PDB chains to EC numbers via SwissProt.

Andrew C R Martin1

  • 1School of Animal and Microbial Science, The University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK. andrew@bioinf.org.uk

Bioinformatics (Oxford, England)
|February 7, 2004
PubMed
Summary

We developed a web server to map Protein Data Bank chains to Enzyme Classification numbers. This tool aids research into protein structure-function relationships by providing queryable and downloadable data.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Understanding protein structure-function relationships is crucial in biological research.
  • Existing methods for mapping protein chains to functional classifications can be complex.
  • The Protein Data Bank (PDB) and Enzyme Classification (EC) numbers are fundamental resources.

Purpose of the Study:

  • To create an automated system for linking Protein Data Bank (PDB) chains to their corresponding Enzyme Classification (EC) numbers.
  • To facilitate research into protein structure-function relationships by providing a direct mapping.
  • To make this mapping data easily accessible and usable for the scientific community.

Main Methods:

  • Development of an automatically updated web server.

Related Experiment Videos

  • Implementation of a queryable interface for accessing the PDB-EC number mapping.
  • Provision of downloadable data in XML and flat file formats.

    • Main Results:

    • An operational web server providing an automated mapping between PDB chains and EC numbers.
    • The mapping is available through a user-friendly query system.
    • Data can be downloaded for offline analysis and integration into other research workflows.

    Conclusions:

    • The developed web server simplifies the process of linking protein structural data with enzymatic function.
    • This resource is valuable for researchers investigating structure-function correlations.
    • The automated and accessible nature of the tool enhances its utility in biological research.