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EXProt: a database for proteins with an experimentally verified function.

Björn M Ursing1, Frank H J van Enckevort, Jack A M Leunissen

  • 1Centre for Molecular and Biomolecular Informatics (CMBI), University of Nijmegen, PO Box 9010, 6500 GL Nijmegen, The Netherlands. ursing@cmbi.kun.nl

Nucleic Acids Research
|December 26, 2001
PubMed
Summary
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EXProt 2.0 is a curated protein database featuring experimentally verified functions from Pseudomonas aeruginosa and Escherichia coli. This resource aids researchers by providing non-redundant protein data with functional annotations and cross-references.

Area of Science:

  • Bioinformatics
  • Proteomics
  • Database Development

Background:

  • Protein function databases are crucial for biological research.
  • Existing databases may contain redundant or unverified entries.
  • A need exists for a curated, non-redundant protein resource.

Purpose of the Study:

  • To present EXProt release 2.0, a curated protein database.
  • To focus on proteins with experimentally verified functions.
  • To consolidate data from multiple sources for improved accessibility.

Main Methods:

  • Collected entries from Pseudomonas aeruginosa community annotation project (PseudoCAP) and Escherichia coli genome and proteome database (GenProtEC).
  • Included translated coding sequences from EMBL nucleotide sequence database for prokaryotes with verified functions.

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  • Assigned unique IDs and compiled species, amino acid sequence, and functional annotation for each entry.

    • Main Results:

    • EXProt release 2.0 contains a non-redundant collection of proteins with experimentally verified functions.
    • Entries include species, amino acid sequence, functional annotation, and links to MEDLINE/PubMed and original databases.
    • The database is indexed in SRS and searchable via BLAST and FASTA on the EXProt web page.

    Conclusions:

    • EXProt provides a valuable, curated resource for researchers seeking proteins with experimentally validated functions.
    • The database facilitates efficient retrieval and analysis of protein information.
    • EXProt enhances the study of prokaryotic proteomes, particularly for E. coli and P. aeruginosa.