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Related Experiment Videos

Mapping PDB chains to UniProtKB entries.

Andrew C R Martin1

  • 1Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK. andrew@bioinf.org.uk

Bioinformatics (Oxford, England)
|September 29, 2005
PubMed
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A new database automatically maps Protein Data Bank (PDB) residues to UniProtKB/SwissProt entries. This resource provides residue-level cross-references, improving protein sequence annotation discoverability.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Proteomics

Background:

  • UniProtKB/SwissProt is a key resource for protein sequence annotations.
  • Existing links to Protein Data Bank (PDB) lack detailed residue-level mapping.
  • A gap exists in identifying UniProtKB/SwissProt entries for specific PDB residues.

Purpose of the Study:

  • To develop an automatically maintained database linking PDB and UniProtKB residues.
  • To provide a comprehensive residue-level mapping between PDB and UniProtKB entries.

Main Methods:

  • Utilized existing PDB-to-UniProtKB and UniProtKB-to-PDB links.
  • Employed a brute-force sequence scan to resolve unannotated PDB chains.
  • Performed sequence alignments between PDB and UniProtKB sequences for residue mapping.

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Main Results:

  • Created an automated database mapping PDB residues to UniProtKB/SwissProt and UniProtKB/trEMBL.
  • Successfully resolved mappings for PDB chains lacking direct annotated links.
  • Established a residue-level correspondence between structural and sequence databases.

Conclusions:

  • The developed resource offers a straightforward method for residue-level cross-referencing.
  • This tool enhances the integration of structural and sequence data in bioinformatics.
  • The database is accessible for interactive querying and download.